[{"publisher":"Oxford University Press","citation":{"ieee":"T. Hausel and M. Thaddeus, “Generators for the cohomology ring of the moduli space of rank 2 higgs bundles,” <i>Proceedings of the London Mathematical Society</i>, vol. 88, no. 3. Oxford University Press, pp. 632–658, 2004.","apa":"Hausel, T., &#38; Thaddeus, M. (2004). Generators for the cohomology ring of the moduli space of rank 2 higgs bundles. <i>Proceedings of the London Mathematical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1112/S0024611503014618\">https://doi.org/10.1112/S0024611503014618</a>","chicago":"Hausel, Tamás, and Michael Thaddeus. “Generators for the Cohomology Ring of the Moduli Space of Rank 2 Higgs Bundles.” <i>Proceedings of the London Mathematical Society</i>. Oxford University Press, 2004. <a href=\"https://doi.org/10.1112/S0024611503014618\">https://doi.org/10.1112/S0024611503014618</a>.","mla":"Hausel, Tamás, and Michael Thaddeus. “Generators for the Cohomology Ring of the Moduli Space of Rank 2 Higgs Bundles.” <i>Proceedings of the London Mathematical Society</i>, vol. 88, no. 3, Oxford University Press, 2004, pp. 632–58, doi:<a href=\"https://doi.org/10.1112/S0024611503014618\">10.1112/S0024611503014618</a>.","ama":"Hausel T, Thaddeus M. Generators for the cohomology ring of the moduli space of rank 2 higgs bundles. <i>Proceedings of the London Mathematical Society</i>. 2004;88(3):632-658. doi:<a href=\"https://doi.org/10.1112/S0024611503014618\">10.1112/S0024611503014618</a>","ista":"Hausel T, Thaddeus M. 2004. Generators for the cohomology ring of the moduli space of rank 2 higgs bundles. Proceedings of the London Mathematical Society. 88(3), 632–658.","short":"T. Hausel, M. Thaddeus, Proceedings of the London Mathematical Society 88 (2004) 632–658."},"doi":"10.1112/S0024611503014618","title":"Generators for the cohomology ring of the moduli space of rank 2 higgs bundles","year":"2004","status":"public","publication":"Proceedings of the London Mathematical Society","oa":1,"publist_id":"5736","type":"journal_article","day":"01","author":[{"id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","first_name":"Tamas","last_name":"Hausel","full_name":"Tamas Hausel"},{"last_name":"Thaddeus","first_name":"Michael","full_name":"Thaddeus, Michael"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/math/0003093"}],"issue":"3","extern":1,"page":"632 - 658","date_updated":"2021-01-12T06:50:55Z","quality_controlled":0,"date_created":"2018-12-11T11:52:10Z","date_published":"2004-05-01T00:00:00Z","volume":88,"intvolume":"        88","publication_status":"published","abstract":[{"lang":"eng","text":"The moduli space of stable vector bundles on a Riemann surface is smooth when the rank and degree are coprime, and is diffeomorphic to the space of unitary connections of central constant curvature. A classic result of Newstead and Atiyah and Bott asserts that its rational cohomology ring is generated by the universal classes, that is, by the Kunneth components of the Chern classes of the universal bundle.\n\nThis paper studies the larger, non-compact moduli space of Higgs bundles, as introduced by Hitchin and Simpson, with values in the canonical bundle K. This is diffeomorphic to the space of all connections of central constant curvature, whether unitary or not. The main result of the paper is that, in the rank 2 case, the rational cohomology ring of this space is again generated by universal classes.\n\nThe spaces of Higgs bundles with values in K(n) for n &gt; 0 turn out to be essential to the story. Indeed, we show that their direct limit has the homotopy type of the classifying space of the gauge group, and hence has cohomology generated by universal classes. 2000 Mathematics Subject Classification 14H60 (primary), 14D20, 14H81, 32Q55, 58D27 (secondary). "}],"month":"05","_id":"1464"},{"day":"14","scopus_import":"1","citation":{"mla":"Campbell, C. J., et al. “Color Micro- and Nanopatterning with Counter-Propagating Reaction-Diffusion Fronts.” <i>Advanced Materials</i>, vol. 16, no. 21, Wiley, 2004, pp. 1912–17, doi:<a href=\"https://doi.org/10.1002/adma.200400383\">10.1002/adma.200400383</a>.","chicago":"Campbell, C. J., M. Fialkowski, Rafal Klajn, I. T. Bensemann, and B. A. Grzybowski. “Color Micro- and Nanopatterning with Counter-Propagating Reaction-Diffusion Fronts.” <i>Advanced Materials</i>. Wiley, 2004. <a href=\"https://doi.org/10.1002/adma.200400383\">https://doi.org/10.1002/adma.200400383</a>.","ieee":"C. J. Campbell, M. Fialkowski, R. Klajn, I. T. Bensemann, and B. A. Grzybowski, “Color micro- and nanopatterning with counter-propagating reaction-diffusion fronts,” <i>Advanced Materials</i>, vol. 16, no. 21. Wiley, pp. 1912–1917, 2004.","apa":"Campbell, C. J., Fialkowski, M., Klajn, R., Bensemann, I. T., &#38; Grzybowski, B. A. (2004). Color micro- and nanopatterning with counter-propagating reaction-diffusion fronts. <i>Advanced Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/adma.200400383\">https://doi.org/10.1002/adma.200400383</a>","short":"C.J. Campbell, M. Fialkowski, R. Klajn, I.T. Bensemann, B.A. Grzybowski, Advanced Materials 16 (2004) 1912–1917.","ista":"Campbell CJ, Fialkowski M, Klajn R, Bensemann IT, Grzybowski BA. 2004. Color micro- and nanopatterning with counter-propagating reaction-diffusion fronts. Advanced Materials. 16(21), 1912–1917.","ama":"Campbell CJ, Fialkowski M, Klajn R, Bensemann IT, Grzybowski BA. Color micro- and nanopatterning with counter-propagating reaction-diffusion fronts. <i>Advanced Materials</i>. 2004;16(21):1912-1917. doi:<a href=\"https://doi.org/10.1002/adma.200400383\">10.1002/adma.200400383</a>"},"keyword":["Mechanical Engineering","Mechanics of Materials","General Materials Science"],"publication":"Advanced Materials","publication_status":"published","abstract":[{"lang":"eng","text":"Thin films of ionically doped gelatin have been color-patterned with submicrometer precision using the wet-stamping technique. Inorganic salts are delivered onto the gelatin surface from an agarose stamp, and diffuse into the gelatine layer, producting deeply colored precipitates. Reaction fronts originating from different features of the stamp cease within < 1 μm of each other, leaving sharp, transparent regions in between."}],"date_created":"2023-08-01T10:39:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        16","volume":16,"extern":"1","author":[{"full_name":"Campbell, C. J.","last_name":"Campbell","first_name":"C. J."},{"full_name":"Fialkowski, M.","last_name":"Fialkowski","first_name":"M."},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","first_name":"Rafal","last_name":"Klajn"},{"full_name":"Bensemann, I. T.","first_name":"I. T.","last_name":"Bensemann"},{"first_name":"B. A.","last_name":"Grzybowski","full_name":"Grzybowski, B. A."}],"type":"journal_article","oa_version":"None","doi":"10.1002/adma.200400383","publisher":"Wiley","status":"public","title":"Color micro- and nanopatterning with counter-propagating reaction-diffusion fronts","year":"2004","publication_identifier":{"issn":["0935-9648"],"eissn":["1521-4095"]},"month":"11","article_processing_charge":"No","_id":"13434","quality_controlled":"1","date_published":"2004-11-14T00:00:00Z","language":[{"iso":"eng"}],"page":"1912-1917","issue":"21","article_type":"original","date_updated":"2023-08-08T12:41:23Z"},{"abstract":[{"text":"Micropatterning of surfaces with several chemicals at different spatial locations usually requires multiple stamping and registration steps. Here, we describe an experimental method based on reaction–diffusion phenomena that allows for simultaneous micropatterning of a substrate with several coloured chemicals. In this method, called wet stamping (WETS), aqueous solutions of two or more inorganic salts are delivered onto a film of dry, ionically doped gelatin from an agarose stamp patterned in bas relief. Once in conformal contact, these salts diffuse into the gelatin, where they react to give deeply coloured precipitates. Separation of colours in the plane of the surface is the consequence of the differences in the diffusion coefficients, the solubility products, and the amounts of different salts delivered from the stamp, and is faithfully reproduced by a theoretical model based on a system of reaction–diffusion partial differential equations. The multicolour micropatterns are useful as non-binary optical elements, and could potentially form the basis of new applications in microseparations and in controlled delivery.","lang":"eng"}],"publication_status":"published","date_created":"2023-08-01T10:39:23Z","intvolume":"         3","volume":3,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"extern":"1","day":"19","scopus_import":"1","keyword":["Mechanical Engineering","Mechanics of Materials","Condensed Matter Physics","General Materials Science","General Chemistry"],"citation":{"chicago":"Klajn, Rafal, Marcin Fialkowski, Igor T. Bensemann, Agnieszka Bitner, C. J. Campbell, Kyle Bishop, Stoyan Smoukov, and Bartosz A. Grzybowski. “Multicolour Micropatterning of Thin Films of Dry Gels.” <i>Nature Materials</i>. Springer Nature, 2004. <a href=\"https://doi.org/10.1038/nmat1231\">https://doi.org/10.1038/nmat1231</a>.","mla":"Klajn, Rafal, et al. “Multicolour Micropatterning of Thin Films of Dry Gels.” <i>Nature Materials</i>, vol. 3, Springer Nature, 2004, pp. 729–35, doi:<a href=\"https://doi.org/10.1038/nmat1231\">10.1038/nmat1231</a>.","apa":"Klajn, R., Fialkowski, M., Bensemann, I. T., Bitner, A., Campbell, C. J., Bishop, K., … Grzybowski, B. A. (2004). Multicolour micropatterning of thin films of dry gels. <i>Nature Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nmat1231\">https://doi.org/10.1038/nmat1231</a>","ieee":"R. Klajn <i>et al.</i>, “Multicolour micropatterning of thin films of dry gels,” <i>Nature Materials</i>, vol. 3. Springer Nature, pp. 729–735, 2004.","ista":"Klajn R, Fialkowski M, Bensemann IT, Bitner A, Campbell CJ, Bishop K, Smoukov S, Grzybowski BA. 2004. Multicolour micropatterning of thin films of dry gels. Nature Materials. 3, 729–735.","ama":"Klajn R, Fialkowski M, Bensemann IT, et al. Multicolour micropatterning of thin films of dry gels. <i>Nature Materials</i>. 2004;3:729-735. doi:<a href=\"https://doi.org/10.1038/nmat1231\">10.1038/nmat1231</a>","short":"R. Klajn, M. Fialkowski, I.T. Bensemann, A. Bitner, C.J. Campbell, K. Bishop, S. Smoukov, B.A. Grzybowski, Nature Materials 3 (2004) 729–735."},"publication":"Nature Materials","publication_identifier":{"eissn":["1476-4660"],"issn":["1476-1122"]},"article_processing_charge":"No","month":"09","_id":"13435","date_published":"2004-09-19T00:00:00Z","quality_controlled":"1","language":[{"iso":"eng"}],"page":"729-735","date_updated":"2023-08-08T12:42:51Z","external_id":{"pmid":["15378052"]},"article_type":"original","author":[{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","first_name":"Rafal","last_name":"Klajn"},{"full_name":"Fialkowski, Marcin","first_name":"Marcin","last_name":"Fialkowski"},{"full_name":"Bensemann, Igor T.","first_name":"Igor T.","last_name":"Bensemann"},{"full_name":"Bitner, Agnieszka","first_name":"Agnieszka","last_name":"Bitner"},{"full_name":"Campbell, C. J.","last_name":"Campbell","first_name":"C. J."},{"full_name":"Bishop, Kyle","last_name":"Bishop","first_name":"Kyle"},{"first_name":"Stoyan","last_name":"Smoukov","full_name":"Smoukov, Stoyan"},{"first_name":"Bartosz A.","last_name":"Grzybowski","full_name":"Grzybowski, Bartosz A."}],"type":"journal_article","oa_version":"None","publisher":"Springer Nature","doi":"10.1038/nmat1231","title":"Multicolour micropatterning of thin films of dry gels","year":"2004","status":"public"},{"publist_id":"6750","doi":"10.1101/gr.2195604","citation":{"short":"C. Castillo Davis, F. Kondrashov, D. Hartl, R. Kulathinal, Genome Research 14 (2004) 802–811.","ista":"Castillo Davis C, Kondrashov F, Hartl D, Kulathinal R. 2004. The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint. Genome Research. 14(5), 802–811.","ama":"Castillo Davis C, Kondrashov F, Hartl D, Kulathinal R. The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint. <i>Genome Research</i>. 2004;14(5):802-811. doi:<a href=\"https://doi.org/10.1101/gr.2195604\">10.1101/gr.2195604</a>","apa":"Castillo Davis, C., Kondrashov, F., Hartl, D., &#38; Kulathinal, R. (2004). The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint. <i>Genome Research</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gr.2195604\">https://doi.org/10.1101/gr.2195604</a>","ieee":"C. Castillo Davis, F. Kondrashov, D. Hartl, and R. Kulathinal, “The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint,” <i>Genome Research</i>, vol. 14, no. 5. Cold Spring Harbor Laboratory Press, pp. 802–811, 2004.","mla":"Castillo Davis, Cristian, et al. “The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint.” <i>Genome Research</i>, vol. 14, no. 5, Cold Spring Harbor Laboratory Press, 2004, pp. 802–11, doi:<a href=\"https://doi.org/10.1101/gr.2195604\">10.1101/gr.2195604</a>.","chicago":"Castillo Davis, Cristian, Fyodor Kondrashov, Daniel Hartl, and Rob Kulathinal. “The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint.” <i>Genome Research</i>. Cold Spring Harbor Laboratory Press, 2004. <a href=\"https://doi.org/10.1101/gr.2195604\">https://doi.org/10.1101/gr.2195604</a>."},"publisher":"Cold Spring Harbor Laboratory Press","acknowledgement":"We thank all members of the Hartl lab for their friendly support and Guillaume Achaz for valuable comments. We also thank the Sanger Institute and the Genome Sequencing Center at Wash- ington University, St. Louis and Lincoln Stein for providing un- finished C. briggsae sequence. Special thanks to the Bauer Center for Genomics Research at Harvard University and Gordon Kindl- mann at the University of Utah Scientific Computing and Imag- ing Institute for computational resources. R.J.K. is financially supported by a postdoctoral fellowship from the Natural Sciences and Engineering Research Council of Canada.\nThe publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 USC section 1734 solely to indicate this fact.","title":"The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint","publication":"Genome Research","year":"2004","status":"public","author":[{"first_name":"Cristian","last_name":"Castillo Davis","full_name":"Castillo-Davis, Cristian I"},{"last_name":"Kondrashov","first_name":"Fyodor","full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"},{"first_name":"Daniel","last_name":"Hartl","full_name":"Hartl, Daniel L"},{"full_name":"Kulathinal, Rob J","first_name":"Rob","last_name":"Kulathinal"}],"type":"journal_article","day":"01","date_created":"2018-12-11T11:49:06Z","quality_controlled":0,"date_published":"2004-05-01T00:00:00Z","intvolume":"        14","volume":14,"extern":1,"page":"802 - 811","issue":"5","date_updated":"2021-01-12T08:21:47Z","abstract":[{"text":"We compare the functional spectrum of protein evolution in two separate animal lineages with respect to two hypotheses: (1) rates of divergence are distributed similarly among functional classes within both lineages, indicating that selective pressure on the proteome is largely independent of organismic-level biological requirements; and (2) rates of divergence are distributed differently among functional classes within each lineage, indicating species-specific selective regimes impact genome-wide substitutional patterns. Integrating comparative genome sequence with data from tissue-specific expressed-sequence-tag (EST) libraries and detailed database annotations, we find a functional genomic signature of rapid evolution and selective constraint shared between mammalian and nematode lineages despite their extensive morphological and ecological differences and distant common ancestry. In both phyla, we find evidence of accelerated evolution among components of molecular systems involved in coevolutionary change. In mammals, lineage-specific fast evolving genes include those involved in reproduction, immunity, and possibly, maternal-fetal conflict. Likelihood ratio tests provide evidence for positive selection in these rapidly evolving functional categories in mammals. In contrast, slowly evolving genes, in terms of amino acid or insertion/deletion (indel) change, in both phyla are involved in core molecular processes such as transcription, translation, and protein transport. Thus, strong purifying selection appears to act on the same core cellular processes in both mammalian and nematode lineages, whereas positive and/or relaxed selection acts on different biological processes in each lineage.","lang":"eng"}],"month":"05","publication_status":"published","_id":"902"},{"publication_status":"published","pmid":1,"extern":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":303,"intvolume":"       303","date_created":"2021-06-04T11:12:35Z","scopus_import":"1","day":"27","publication":"Science","citation":{"short":"S.W.-L. Chan, D. Zilberman,  Zhixin Xie,  Lisa K. Johansen, J.C. Carrington, S.E. Jacobsen, Science 303 (2004) 1336.","ama":"Chan SW-L, Zilberman D, Xie  Zhixin, Johansen  Lisa K., Carrington JC, Jacobsen SE. RNA silencing genes control de novo DNA methylation. <i>Science</i>. 2004;303(5662):1336. doi:<a href=\"https://doi.org/10.1126/science.1095989\">10.1126/science.1095989</a>","ista":"Chan SW-L, Zilberman D, Xie  Zhixin, Johansen  Lisa K., Carrington JC, Jacobsen SE. 2004. RNA silencing genes control de novo DNA methylation. Science. 303(5662), 1336.","mla":"Chan, Simon W. L., et al. “RNA Silencing Genes Control de Novo DNA Methylation.” <i>Science</i>, vol. 303, no. 5662, American Association for the Advancement of Science, 2004, p. 1336, doi:<a href=\"https://doi.org/10.1126/science.1095989\">10.1126/science.1095989</a>.","chicago":"Chan, Simon W.-L., Daniel Zilberman,  Zhixin Xie,  Lisa K. Johansen, James C. Carrington, and Steven E. Jacobsen. “RNA Silencing Genes Control de Novo DNA Methylation.” <i>Science</i>. American Association for the Advancement of Science, 2004. <a href=\"https://doi.org/10.1126/science.1095989\">https://doi.org/10.1126/science.1095989</a>.","apa":"Chan, S. W.-L., Zilberman, D., Xie,  Zhixin, Johansen,  Lisa K., Carrington, J. C., &#38; Jacobsen, S. E. (2004). RNA silencing genes control de novo DNA methylation. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1095989\">https://doi.org/10.1126/science.1095989</a>","ieee":"S. W.-L. Chan, D. Zilberman,  Zhixin Xie,  Lisa K. Johansen, J. C. Carrington, and S. E. Jacobsen, “RNA silencing genes control de novo DNA methylation,” <i>Science</i>, vol. 303, no. 5662. American Association for the Advancement of Science, p. 1336, 2004."},"department":[{"_id":"DaZi"}],"keyword":["Multidisciplinary"],"_id":"9454","month":"02","article_processing_charge":"No","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"article_type":"original","date_updated":"2021-12-14T09:13:53Z","external_id":{"pmid":["14988555"]},"issue":"5662","page":"1336","language":[{"iso":"eng"}],"date_published":"2004-02-27T00:00:00Z","quality_controlled":"1","type":"journal_article","author":[{"last_name":"Chan","first_name":"Simon W.-L.","full_name":"Chan, Simon W.-L."},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman","full_name":"Zilberman, Daniel"},{"first_name":" Zhixin","last_name":"Xie","full_name":"Xie,  Zhixin"},{"full_name":"Johansen,  Lisa K.","last_name":"Johansen","first_name":" Lisa K."},{"last_name":"Carrington","first_name":"James C.","full_name":"Carrington, James C."},{"full_name":"Jacobsen, Steven E.","last_name":"Jacobsen","first_name":"Steven E."}],"status":"public","title":"RNA silencing genes control de novo DNA methylation","year":"2004","doi":"10.1126/science.1095989","publisher":"American Association for the Advancement of Science","oa_version":"None"},{"day":"13","scopus_import":"1","department":[{"_id":"DaZi"}],"citation":{"chicago":"Zilberman, Daniel, Xiaofeng Cao, Lisa K. Johansen, Zhixin Xie, James C. Carrington, and Steven E. Jacobsen. “Role of Arabidopsis ARGONAUTE4 in RNA-Directed DNA Methylation Triggered by Inverted Repeats.” <i>Current Biology</i>. Elsevier, 2004. <a href=\"https://doi.org/10.1016/j.cub.2004.06.055\">https://doi.org/10.1016/j.cub.2004.06.055</a>.","mla":"Zilberman, Daniel, et al. “Role of Arabidopsis ARGONAUTE4 in RNA-Directed DNA Methylation Triggered by Inverted Repeats.” <i>Current Biology</i>, vol. 14, no. 13, Elsevier, 2004, pp. 1214–20, doi:<a href=\"https://doi.org/10.1016/j.cub.2004.06.055\">10.1016/j.cub.2004.06.055</a>.","ieee":"D. Zilberman, X. Cao, L. K. Johansen, Z. Xie, J. C. Carrington, and S. E. Jacobsen, “Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats,” <i>Current Biology</i>, vol. 14, no. 13. Elsevier, pp. 1214–1220, 2004.","apa":"Zilberman, D., Cao, X., Johansen, L. K., Xie, Z., Carrington, J. C., &#38; Jacobsen, S. E. (2004). Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2004.06.055\">https://doi.org/10.1016/j.cub.2004.06.055</a>","ama":"Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. <i>Current Biology</i>. 2004;14(13):1214-1220. doi:<a href=\"https://doi.org/10.1016/j.cub.2004.06.055\">10.1016/j.cub.2004.06.055</a>","ista":"Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. 2004. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Current Biology. 14(13), 1214–1220.","short":"D. Zilberman, X. Cao, L.K. Johansen, Z. Xie, J.C. Carrington, S.E. Jacobsen, Current Biology 14 (2004) 1214–1220."},"publication":"Current Biology","oa":1,"publication_status":"published","abstract":[{"text":"In a number of organisms, transgenes containing transcribed inverted repeats (IRs) that produce hairpin RNA can trigger RNA-mediated silencing, which is associated with 21-24 nucleotide small interfering RNAs (siRNAs). In plants, IR-driven RNA silencing also causes extensive cytosine methylation of homologous DNA in both the transgene \"trigger\" and any other homologous DNA sequences--\"targets\". Endogenous genomic sequences, including transposable elements and repeated elements, are also subject to RNA-mediated silencing. The RNA silencing gene ARGONAUTE4 (AGO4) is required for maintenance of DNA methylation at several endogenous loci and for the establishment of methylation at the FWA gene. Here, we show that mutation of AGO4 substantially reduces the maintenance of DNA methylation triggered by IR transgenes, but AGO4 loss-of-function does not block the initiation of DNA methylation by IRs. AGO4 primarily affects non-CG methylation of the target sequences, while the IR trigger sequences lose methylation in all sequence contexts. Finally, we find that AGO4 and the DRM methyltransferase genes are required for maintenance of siRNAs at a subset of endogenous sequences, but AGO4 is not required for the accumulation of IR-induced siRNAs or a number of endogenous siRNAs, suggesting that AGO4 may function downstream of siRNA production.","lang":"eng"}],"pmid":1,"extern":"1","date_created":"2021-06-07T10:33:00Z","intvolume":"        14","volume":14,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","author":[{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","last_name":"Zilberman","first_name":"Daniel"},{"full_name":"Cao, Xiaofeng","last_name":"Cao","first_name":"Xiaofeng"},{"last_name":"Johansen","first_name":"Lisa K.","full_name":"Johansen, Lisa K."},{"first_name":"Zhixin","last_name":"Xie","full_name":"Xie, Zhixin"},{"first_name":"James C.","last_name":"Carrington","full_name":"Carrington, James C."},{"last_name":"Jacobsen","first_name":"Steven E.","full_name":"Jacobsen, Steven E."}],"main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2004.06.055","open_access":"1"}],"publisher":"Elsevier","doi":"10.1016/j.cub.2004.06.055","status":"public","title":"Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats","year":"2004","oa_version":"Published Version","article_processing_charge":"No","month":"07","_id":"9493","publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"page":"1214-1220","issue":"13","external_id":{"pmid":["15242620 "]},"date_updated":"2021-12-14T08:52:00Z","article_type":"original","quality_controlled":"1","date_published":"2004-07-13T00:00:00Z","language":[{"iso":"eng"}]},{"day":"16","scopus_import":"1","oa":1,"publication":"Genome Biology","citation":{"ista":"Zilberman D, Henikoff S. 2004. Silencing of transposons in plant genomes: kick them when they’re down. Genome Biology. 5(12), 249.","ama":"Zilberman D, Henikoff S. Silencing of transposons in plant genomes: kick them when they’re down. <i>Genome Biology</i>. 2004;5(12). doi:<a href=\"https://doi.org/10.1186/gb-2004-5-12-249\">10.1186/gb-2004-5-12-249</a>","short":"D. Zilberman, S. Henikoff, Genome Biology 5 (2004).","chicago":"Zilberman, Daniel, and Steven Henikoff. “Silencing of Transposons in Plant Genomes: Kick Them When They’re Down.” <i>Genome Biology</i>. Springer Nature, 2004. <a href=\"https://doi.org/10.1186/gb-2004-5-12-249\">https://doi.org/10.1186/gb-2004-5-12-249</a>.","mla":"Zilberman, Daniel, and Steven Henikoff. “Silencing of Transposons in Plant Genomes: Kick Them When They’re Down.” <i>Genome Biology</i>, vol. 5, no. 12, 249, Springer Nature, 2004, doi:<a href=\"https://doi.org/10.1186/gb-2004-5-12-249\">10.1186/gb-2004-5-12-249</a>.","ieee":"D. Zilberman and S. Henikoff, “Silencing of transposons in plant genomes: kick them when they’re down,” <i>Genome Biology</i>, vol. 5, no. 12. Springer Nature, 2004.","apa":"Zilberman, D., &#38; Henikoff, S. (2004). Silencing of transposons in plant genomes: kick them when they’re down. <i>Genome Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/gb-2004-5-12-249\">https://doi.org/10.1186/gb-2004-5-12-249</a>"},"department":[{"_id":"DaZi"}],"article_number":"249","abstract":[{"text":"Recent progress in understanding the silencing of transposable elements in the model plant Arabidopsis has revealed an interplay between DNA methylation, histone methylation and small interfering RNAs. DNA and histone methylation are not always sufficient to maintain silencing, and RNA-based reinforcement can be needed to maintain as well as initiate it.","lang":"eng"}],"publication_status":"published","volume":5,"intvolume":"         5","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2021-06-07T12:58:06Z","extern":"1","pmid":1,"main_file_link":[{"url":"https://doi.org/10.1186/gb-2004-5-12-249","open_access":"1"}],"author":[{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"last_name":"Henikoff","first_name":"Steven","full_name":"Henikoff, Steven"}],"type":"journal_article","oa_version":"Published Version","status":"public","year":"2004","title":"Silencing of transposons in plant genomes: kick them when they're down","publisher":"Springer Nature","doi":"10.1186/gb-2004-5-12-249","publication_identifier":{"issn":["1474-760X"],"eissn":["1465-6906"]},"_id":"9511","article_processing_charge":"No","month":"11","language":[{"iso":"eng"}],"date_published":"2004-11-16T00:00:00Z","quality_controlled":"1","external_id":{"pmid":["15575975"]},"date_updated":"2021-12-14T08:44:24Z","article_type":"review","issue":"12"},{"day":"24","scopus_import":"1","citation":{"short":"Z. Xie, L.K. Johansen, A.M. Gustafson, K.D. Kasschau, A.D. Lellis, D. Zilberman, S.E. Jacobsen, J.C. Carrington, PLoS Biology 2 (2004) 0642–0652.","ama":"Xie Z, Johansen LK, Gustafson AM, et al. Genetic and functional diversification of small RNA pathways in plants. <i>PLoS Biology</i>. 2004;2(5):0642-0652. doi:<a href=\"https://doi.org/10.1371/journal.pbio.0020104\">10.1371/journal.pbio.0020104</a>","ista":"Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC. 2004. Genetic and functional diversification of small RNA pathways in plants. PLoS Biology. 2(5), 0642–0652.","mla":"Xie, Zhixin, et al. “Genetic and Functional Diversification of Small RNA Pathways in Plants.” <i>PLoS Biology</i>, vol. 2, no. 5, Public Library of Science, 2004, pp. 0642–52, doi:<a href=\"https://doi.org/10.1371/journal.pbio.0020104\">10.1371/journal.pbio.0020104</a>.","chicago":"Xie, Zhixin, Lisa K. Johansen, Adam M. Gustafson, Kristin D. Kasschau, Andrew D.  Lellis, Daniel Zilberman, Steven E. Jacobsen, and James C. Carrington. “Genetic and Functional Diversification of Small RNA Pathways in Plants.” <i>PLoS Biology</i>. Public Library of Science, 2004. <a href=\"https://doi.org/10.1371/journal.pbio.0020104\">https://doi.org/10.1371/journal.pbio.0020104</a>.","apa":"Xie, Z., Johansen, L. K., Gustafson, A. M., Kasschau, K. D., Lellis, A. D., Zilberman, D., … Carrington, J. C. (2004). Genetic and functional diversification of small RNA pathways in plants. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.0020104\">https://doi.org/10.1371/journal.pbio.0020104</a>","ieee":"Z. Xie <i>et al.</i>, “Genetic and functional diversification of small RNA pathways in plants,” <i>PLoS Biology</i>, vol. 2, no. 5. Public Library of Science, pp. 0642–0652, 2004."},"department":[{"_id":"DaZi"}],"publication":"PLoS Biology","oa":1,"publication_status":"published","abstract":[{"lang":"eng","text":"Multicellular eukaryotes produce small RNA molecules (approximately 21–24 nucleotides) of two general types, microRNA (miRNA) and short interfering RNA (siRNA). They collectively function as sequence-specific guides to silence or regulate genes, transposons, and viruses and to modify chromatin and genome structure. Formation or activity of small RNAs requires factors belonging to gene families that encode DICER (or DICER-LIKE [DCL]) and ARGONAUTE proteins and, in the case of some siRNAs, RNA-dependent RNA polymerase (RDR) proteins. Unlike many animals, plants encode multiple DCL and RDR proteins. Using a series of insertion mutants of Arabidopsis thaliana, unique functions for three DCL proteins in miRNA (DCL1), endogenous siRNA (DCL3), and viral siRNA (DCL2) biogenesis were identified. One RDR protein (RDR2) was required for all endogenous siRNAs analyzed. The loss of endogenous siRNA in dcl3 and rdr2 mutants was associated with loss of heterochromatic marks and increased transcript accumulation at some loci. Defects in siRNA-generation activity in response to turnip crinkle virus in dcl2 mutant plants correlated with increased virus susceptibility. We conclude that proliferation and diversification of DCL and RDR genes during evolution of plants contributed to specialization of small RNA-directed pathways for development, chromatin structure, and defense."}],"extern":"1","pmid":1,"date_created":"2021-06-07T14:12:08Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":2,"intvolume":"         2","type":"journal_article","author":[{"last_name":"Xie","first_name":"Zhixin","full_name":"Xie, Zhixin"},{"last_name":"Johansen","first_name":"Lisa K.","full_name":"Johansen, Lisa K."},{"full_name":"Gustafson, Adam M.","first_name":"Adam M.","last_name":"Gustafson"},{"last_name":"Kasschau","first_name":"Kristin D.","full_name":"Kasschau, Kristin D."},{"full_name":"Lellis, Andrew D. ","last_name":"Lellis","first_name":"Andrew D. "},{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"full_name":"Jacobsen, Steven E.","first_name":"Steven E.","last_name":"Jacobsen"},{"last_name":"Carrington","first_name":"James C.","full_name":"Carrington, James C."}],"main_file_link":[{"url":"https://doi.org/10.1371/journal.pbio.0020104","open_access":"1"}],"doi":"10.1371/journal.pbio.0020104","publisher":"Public Library of Science","year":"2004","status":"public","title":"Genetic and functional diversification of small RNA pathways in plants","oa_version":"Published Version","month":"02","article_processing_charge":"No","_id":"9517","publication_identifier":{"issn":["1544-9173"],"eissn":["1545-7885"]},"page":"0642-0652","issue":"5","article_type":"original","date_updated":"2021-12-14T08:43:57Z","external_id":{"pmid":["15024409"]},"quality_controlled":"1","date_published":"2004-02-24T00:00:00Z","language":[{"iso":"eng"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"      3142","volume":3142,"language":[{"iso":"eng"}],"date_created":"2022-08-11T12:38:58Z","date_published":"2004-07-01T00:00:00Z","quality_controlled":"1","date_updated":"2023-02-13T11:45:25Z","page":"3","extern":"1","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"]},"_id":"11800","publication_status":"published","month":"07","abstract":[{"lang":"eng","text":"Web search engines have emerged as one of the central applications on the Internet. In fact, search has become one of the most important activities that people engage in on the the Internet. Even beyond becoming the number one source of information, a growing number of businesses are depending on web search engines for customer acquisition.\r\n\r\nThe first generation of web search engines used text-only retrieval techniques. Google revolutionized the field by deploying the PageRank technology – an eigenvector-based analysis of the hyperlink structure – to analyze the web in order to produce relevant results. Moving forward, our goal is to achieve a better understanding of a page with a view towards producing even more relevant results."}],"article_processing_charge":"No","oa_version":"None","year":"2004","title":"The past, present, and future of web search engines","publication":"31st International Colloquium on Automata, Languages and Programming","status":"public","citation":{"mla":"Henzinger, Monika H. “The Past, Present, and Future of Web Search Engines.” <i>31st International Colloquium on Automata, Languages and Programming</i>, vol. 3142, Springer Nature, 2004, p. 3, doi:<a href=\"https://doi.org/10.1007/978-3-540-27836-8_2\">10.1007/978-3-540-27836-8_2</a>.","chicago":"Henzinger, Monika H. “The Past, Present, and Future of Web Search Engines.” In <i>31st International Colloquium on Automata, Languages and Programming</i>, 3142:3. Springer Nature, 2004. <a href=\"https://doi.org/10.1007/978-3-540-27836-8_2\">https://doi.org/10.1007/978-3-540-27836-8_2</a>.","apa":"Henzinger, M. H. (2004). The past, present, and future of web search engines. In <i>31st International Colloquium on Automata, Languages and Programming</i> (Vol. 3142, p. 3). Turku, Finland: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-540-27836-8_2\">https://doi.org/10.1007/978-3-540-27836-8_2</a>","ieee":"M. H. Henzinger, “The past, present, and future of web search engines,” in <i>31st International Colloquium on Automata, Languages and Programming</i>, Turku, Finland, 2004, vol. 3142, p. 3.","short":"M.H. Henzinger, in:, 31st International Colloquium on Automata, Languages and Programming, Springer Nature, 2004, p. 3.","ama":"Henzinger MH. The past, present, and future of web search engines. In: <i>31st International Colloquium on Automata, Languages and Programming</i>. Vol 3142. Springer Nature; 2004:3. doi:<a href=\"https://doi.org/10.1007/978-3-540-27836-8_2\">10.1007/978-3-540-27836-8_2</a>","ista":"Henzinger MH. 2004. The past, present, and future of web search engines. 31st International Colloquium on Automata, Languages and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LNCS, vol. 3142, 3."},"doi":"10.1007/978-3-540-27836-8_2","publisher":"Springer Nature","author":[{"orcid":"0000-0002-5008-6530","last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"}],"alternative_title":["LNCS"],"day":"01","scopus_import":"1","type":"conference","conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","end_date":"2004-07-16","start_date":"2004-07-12","location":"Turku, Finland"}},{"intvolume":"      3221","volume":3221,"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","date_published":"2004-09-01T00:00:00Z","date_created":"2022-08-11T13:18:05Z","date_updated":"2023-02-13T11:47:26Z","page":"3","extern":"1","publication_identifier":{"issn":["0302-9743"],"isbn":[" 3540230254"],"eissn":["1611-3349"]},"_id":"11801","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Web search engines have emerged as one of the central applications on the internet. In fact, search has become one of the most important activities that people engage in on the Internet. Even beyond becoming the number one source of information, a growing number of businesses are depending on web search engines for customer acquisition. In this talk I will brief review the history of web search engines: The first generation of web search engines used text-only retrieval techniques. Google revolutionized the field by deploying the PageRank technology – an eigenvector-based analysis of the hyperlink structure- to analyze the web in order to produce relevant results. Moving forward, our goal is to achieve a better understanding of a page with a view towards producing even more relevant results.\r\n\r\nGoogle is powered by a large number of PCs. Using this infrastructure and striving to be as efficient as possible poses challenging systems problems but also various algorithmic challenges. I will discuss some of them in my talk."}],"month":"09","publication_status":"published","oa_version":"None","year":"2004","title":"Algorithmic aspects of web search engines","publication":"2th Annual European Symposium on Algorithms","status":"public","publisher":"Springer Nature","citation":{"short":"M.H. Henzinger, in:, 2th Annual European Symposium on Algorithms, Springer Nature, 2004, p. 3.","ama":"Henzinger MH. Algorithmic aspects of web search engines. In: <i>2th Annual European Symposium on Algorithms</i>. Vol 3221. Springer Nature; 2004:3. doi:<a href=\"https://doi.org/10.1007/978-3-540-30140-0_2\">10.1007/978-3-540-30140-0_2</a>","ista":"Henzinger MH. 2004. Algorithmic aspects of web search engines. 2th Annual European Symposium on Algorithms. ESA: European Symposium on Algorithms, LNCS, vol. 3221, 3.","mla":"Henzinger, Monika H. “Algorithmic Aspects of Web Search Engines.” <i>2th Annual European Symposium on Algorithms</i>, vol. 3221, Springer Nature, 2004, p. 3, doi:<a href=\"https://doi.org/10.1007/978-3-540-30140-0_2\">10.1007/978-3-540-30140-0_2</a>.","chicago":"Henzinger, Monika H. “Algorithmic Aspects of Web Search Engines.” In <i>2th Annual European Symposium on Algorithms</i>, 3221:3. Springer Nature, 2004. <a href=\"https://doi.org/10.1007/978-3-540-30140-0_2\">https://doi.org/10.1007/978-3-540-30140-0_2</a>.","ieee":"M. H. Henzinger, “Algorithmic aspects of web search engines,” in <i>2th Annual European Symposium on Algorithms</i>, Bergen, Norway, 2004, vol. 3221, p. 3.","apa":"Henzinger, M. H. (2004). Algorithmic aspects of web search engines. In <i>2th Annual European Symposium on Algorithms</i> (Vol. 3221, p. 3). Bergen, Norway: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-540-30140-0_2\">https://doi.org/10.1007/978-3-540-30140-0_2</a>"},"doi":"10.1007/978-3-540-30140-0_2","author":[{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530"}],"scopus_import":"1","day":"01","alternative_title":["LNCS"],"conference":{"start_date":"2004-09-14","name":"ESA: European Symposium on Algorithms","end_date":"2004-09-17","location":"Bergen, Norway"},"type":"conference"},{"publication_identifier":{"issn":["0277-786X"]},"_id":"11859","article_processing_charge":"No","publication_status":"published","abstract":[{"lang":"eng","text":"In this article we describe the approach taken by the first web search engines, discuss the state of the art, and present some of the challenges for the future."}],"month":"01","intvolume":"      5296","language":[{"iso":"eng"}],"volume":5296,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","date_created":"2022-08-16T08:46:41Z","date_published":"2004-01-01T00:00:00Z","date_updated":"2023-02-17T10:05:19Z","page":"23 - 26","extern":"1","author":[{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530"}],"day":"01","scopus_import":"1","conference":{"start_date":"2004-01-21","end_date":"2004-01-22","name":"Document Recognition and Retrieval XI","location":"San Jose, CA, United States"},"type":"conference","oa_version":"None","status":"public","publication":"SPIE Proceedings","year":"2004","title":"The past, present, and future of web information retrieval","publisher":"Society of Photo-Optical Instrumentation Engineers","citation":{"short":"M.H. Henzinger, in:, SPIE Proceedings, Society of Photo-Optical Instrumentation Engineers, 2004, pp. 23–26.","ista":"Henzinger MH. 2004. The past, present, and future of web information retrieval. SPIE Proceedings. Document Recognition and Retrieval XI vol. 5296, 23–26.","ama":"Henzinger MH. The past, present, and future of web information retrieval. In: <i>SPIE Proceedings</i>. Vol 5296. Society of Photo-Optical Instrumentation Engineers; 2004:23-26. doi:<a href=\"https://doi.org/10.1117/12.537534\">10.1117/12.537534</a>","mla":"Henzinger, Monika H. “The Past, Present, and Future of Web Information Retrieval.” <i>SPIE Proceedings</i>, vol. 5296, Society of Photo-Optical Instrumentation Engineers, 2004, pp. 23–26, doi:<a href=\"https://doi.org/10.1117/12.537534\">10.1117/12.537534</a>.","chicago":"Henzinger, Monika H. “The Past, Present, and Future of Web Information Retrieval.” In <i>SPIE Proceedings</i>, 5296:23–26. Society of Photo-Optical Instrumentation Engineers, 2004. <a href=\"https://doi.org/10.1117/12.537534\">https://doi.org/10.1117/12.537534</a>.","apa":"Henzinger, M. H. (2004). The past, present, and future of web information retrieval. In <i>SPIE Proceedings</i> (Vol. 5296, pp. 23–26). San Jose, CA, United States: Society of Photo-Optical Instrumentation Engineers. <a href=\"https://doi.org/10.1117/12.537534\">https://doi.org/10.1117/12.537534</a>","ieee":"M. H. Henzinger, “The past, present, and future of web information retrieval,” in <i>SPIE Proceedings</i>, San Jose, CA, United States, 2004, vol. 5296, pp. 23–26."},"doi":"10.1117/12.537534"},{"abstract":[{"text":"The World Wide Web provides a unprecedented opportunity to automatically analyze a large sample of interests and activity in the world. We discuss methods for extracting knowledge from the web by randomly sampling and analyzing hosts and pages, and by analyzing the link structure of the web and how links accumulate over time. A variety of interesting and valuable information can be extracted, such as the distribution of web pages over domains, the distribution of interest in different areas, communities related to different topics, the nature of competition in different categories of sites, and the degree of communication between different communities or countries.","lang":"eng"}],"publication_status":"published","extern":"1","pmid":1,"volume":101,"intvolume":"       101","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-08-16T13:06:10Z","scopus_import":"1","day":"06","publication":"Proceedings of the National Academy of Sciences","citation":{"ista":"Henzinger MH, Lawrence S. 2004. Extracting knowledge from the World Wide Web. Proceedings of the National Academy of Sciences. 101(suppl_1), 5186–5191.","ama":"Henzinger MH, Lawrence S. Extracting knowledge from the World Wide Web. <i>Proceedings of the National Academy of Sciences</i>. 2004;101(suppl_1):5186-5191. doi:<a href=\"https://doi.org/10.1073/pnas.0307528100\">10.1073/pnas.0307528100</a>","short":"M.H. Henzinger, S. Lawrence, Proceedings of the National Academy of Sciences 101 (2004) 5186–5191.","ieee":"M. H. Henzinger and S. Lawrence, “Extracting knowledge from the World Wide Web,” <i>Proceedings of the National Academy of Sciences</i>, vol. 101, no. suppl_1. Proceedings of the National Academy of Sciences, pp. 5186–5191, 2004.","apa":"Henzinger, M. H., &#38; Lawrence, S. (2004). Extracting knowledge from the World Wide Web. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0307528100\">https://doi.org/10.1073/pnas.0307528100</a>","chicago":"Henzinger, Monika H, and Steve Lawrence. “Extracting Knowledge from the World Wide Web.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2004. <a href=\"https://doi.org/10.1073/pnas.0307528100\">https://doi.org/10.1073/pnas.0307528100</a>.","mla":"Henzinger, Monika H., and Steve Lawrence. “Extracting Knowledge from the World Wide Web.” <i>Proceedings of the National Academy of Sciences</i>, vol. 101, no. suppl_1, Proceedings of the National Academy of Sciences, 2004, pp. 5186–91, doi:<a href=\"https://doi.org/10.1073/pnas.0307528100\">10.1073/pnas.0307528100</a>."},"oa":1,"_id":"11877","article_processing_charge":"No","month":"04","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"date_updated":"2023-02-17T12:21:43Z","external_id":{"pmid":["14745041"]},"article_type":"original","page":"5186-5191","issue":"suppl_1","language":[{"iso":"eng"}],"quality_controlled":"1","date_published":"2004-04-06T00:00:00Z","type":"journal_article","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC387294/","open_access":"1"}],"author":[{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H"},{"last_name":"Lawrence","first_name":"Steve","full_name":"Lawrence, Steve"}],"status":"public","year":"2004","title":"Extracting knowledge from the World Wide Web","publisher":"Proceedings of the National Academy of Sciences","doi":"10.1073/pnas.0307528100","oa_version":"Published Version"},{"scopus_import":"1","citation":{"short":"Z. Liao, M. Chen, Y. Gong, L. Guo, Q. Tan, X. Feng, X. Sun, F. Tan, K. Tang, DNA Sequence 15 (2004) 153–158.","ama":"Liao Z, Chen M, Gong Y, et al. A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. <i>DNA Sequence</i>. 2004;15(2):153-158. doi:<a href=\"https://doi.org/10.1080/10425170410001667348\">10.1080/10425170410001667348</a>","ista":"Liao Z, Chen M, Gong Y, Guo L, Tan Q, Feng X, Sun X, Tan F, Tang K. 2004. A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. DNA Sequence. 15(2), 153–158.","mla":"Liao, Zhihua, et al. “A New Geranylgeranyl Diphosphate Synthase Gene from Ginkgo Biloba, Which Intermediates the Biosynthesis of the Key Precursor for Ginkgolides.” <i>DNA Sequence</i>, vol. 15, no. 2, Informa UK Limited, 2004, pp. 153–58, doi:<a href=\"https://doi.org/10.1080/10425170410001667348\">10.1080/10425170410001667348</a>.","chicago":"Liao, Zhihua, Min Chen, Yifu Gong, Liang Guo, Qiumin Tan, Xiaoqi Feng, Xiaofen Sun, Feng Tan, and Kexuan Tang. “A New Geranylgeranyl Diphosphate Synthase Gene from Ginkgo Biloba, Which Intermediates the Biosynthesis of the Key Precursor for Ginkgolides.” <i>DNA Sequence</i>. Informa UK Limited, 2004. <a href=\"https://doi.org/10.1080/10425170410001667348\">https://doi.org/10.1080/10425170410001667348</a>.","apa":"Liao, Z., Chen, M., Gong, Y., Guo, L., Tan, Q., Feng, X., … Tang, K. (2004). A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. <i>DNA Sequence</i>. Informa UK Limited. <a href=\"https://doi.org/10.1080/10425170410001667348\">https://doi.org/10.1080/10425170410001667348</a>","ieee":"Z. Liao <i>et al.</i>, “A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides,” <i>DNA Sequence</i>, vol. 15, no. 2. Informa UK Limited, pp. 153–158, 2004."},"department":[{"_id":"XiFe"}],"keyword":["Endocrinology","Genetics","Molecular Biology","Biochemistry"],"publication":"DNA Sequence","publication_status":"published","abstract":[{"lang":"eng","text":"Geranylgeranyl diphosphate synthase (GGPPS, EC: 2.5.1.29) catalyzes the biosynthesis of geranylgeranyl diphosphate (GGPP), which is a key precursor for ginkgolide biosynthesis. Here we reported for the first time the cloning of a new full-length cDNA encoding GGPPS from the living fossil plant Ginkgo biloba. The full-length cDNA encoding G. biloba GGPPS (designated as GbGGPPS) was 1657bp long and contained a 1176bp open reading frame encoding a 391 amino acid protein. Comparative analysis showed that GbGGPPS possessed a 79 amino acid transit peptide at its N-terminal, which directed GbGGPPS to target to the plastids. Bioinformatic analysis revealed that GbGGPPS was a member of polyprenyltransferases with two highly conserved aspartate-rich motifs like other plant GGPPSs. Phylogenetic tree analysis indicated that plant GGPPSs could be classified into two groups, angiosperm and gymnosperm GGPPSs, while GbGGPPS had closer relationship with gymnosperm plant GGPPSs."}],"date_created":"2023-01-16T09:24:50Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        15","volume":15,"pmid":1,"extern":"1","author":[{"first_name":"Zhihua","last_name":"Liao","full_name":"Liao, Zhihua"},{"full_name":"Chen, Min","first_name":"Min","last_name":"Chen"},{"last_name":"Gong","first_name":"Yifu","full_name":"Gong, Yifu"},{"first_name":"Liang","last_name":"Guo","full_name":"Guo, Liang"},{"first_name":"Qiumin","last_name":"Tan","full_name":"Tan, Qiumin"},{"orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","last_name":"Feng"},{"full_name":"Sun, Xiaofen","first_name":"Xiaofen","last_name":"Sun"},{"first_name":"Feng","last_name":"Tan","full_name":"Tan, Feng"},{"full_name":"Tang, Kexuan","first_name":"Kexuan","last_name":"Tang"}],"type":"journal_article","oa_version":"None","doi":"10.1080/10425170410001667348","publisher":"Informa UK Limited","acknowledgement":"This study was financially supported by China National High-Tech “863” Program. The authors are very thankful to Dr Li Wang (School of Life Sciences, Fudan University, Shanghai, China) for her kind help with constructing the phylogenetic tree.","title":"A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides","status":"public","year":"2004","publication_identifier":{"issn":["1042-5179"]},"article_processing_charge":"No","_id":"12203","quality_controlled":"1","date_published":"2004-01-01T00:00:00Z","language":[{"iso":"eng"}],"page":"153-158","issue":"2","article_type":"original","date_updated":"2023-05-08T10:58:29Z","external_id":{"pmid":["15352294"]}},{"type":"journal_article","author":[{"full_name":"Strasser, Ulrich","last_name":"Strasser","first_name":"Ulrich"},{"first_name":"Javier","last_name":"Corripio","full_name":"Corripio, Javier"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca","first_name":"Francesca","last_name":"Pellicciotti"},{"full_name":"Burlando, Paolo","last_name":"Burlando","first_name":"Paolo"},{"first_name":"Ben","last_name":"Brock","full_name":"Brock, Ben"},{"full_name":"Funk, Martin","first_name":"Martin","last_name":"Funk"}],"publisher":"American Geophysical Union","doi":"10.1029/2003jd003973","year":"2004","status":"public","title":"Spatial and temporal variability of meteorological variables at Haut Glacier d'Arolla (Switzerland) during the ablation season 2001: Measurements and simulations","oa_version":"None","article_processing_charge":"No","month":"02","_id":"12658","publication_identifier":{"issn":["0148-0227"]},"issue":"D3","date_updated":"2023-02-20T08:40:21Z","article_type":"original","date_published":"2004-02-16T00:00:00Z","quality_controlled":"1","language":[{"iso":"eng"}],"scopus_import":"1","day":"16","keyword":["Paleontology","Space and Planetary Science","Earth and Planetary Sciences (miscellaneous)","Atmospheric Science","Earth-Surface Processes","Geochemistry and Petrology","Soil Science","Water Science and Technology","Ecology","Aquatic Science","Forestry","Oceanography","Geophysics"],"citation":{"mla":"Strasser, Ulrich, et al. “Spatial and Temporal Variability of Meteorological Variables at Haut Glacier d’Arolla (Switzerland) during the Ablation Season 2001: Measurements and Simulations.” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 109, no. D3, D03103, American Geophysical Union, 2004, doi:<a href=\"https://doi.org/10.1029/2003jd003973\">10.1029/2003jd003973</a>.","chicago":"Strasser, Ulrich, Javier Corripio, Francesca Pellicciotti, Paolo Burlando, Ben Brock, and Martin Funk. “Spatial and Temporal Variability of Meteorological Variables at Haut Glacier d’Arolla (Switzerland) during the Ablation Season 2001: Measurements and Simulations.” <i>Journal of Geophysical Research: Atmospheres</i>. American Geophysical Union, 2004. <a href=\"https://doi.org/10.1029/2003jd003973\">https://doi.org/10.1029/2003jd003973</a>.","apa":"Strasser, U., Corripio, J., Pellicciotti, F., Burlando, P., Brock, B., &#38; Funk, M. (2004). Spatial and temporal variability of meteorological variables at Haut Glacier d’Arolla (Switzerland) during the ablation season 2001: Measurements and simulations. <i>Journal of Geophysical Research: Atmospheres</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2003jd003973\">https://doi.org/10.1029/2003jd003973</a>","ieee":"U. Strasser, J. Corripio, F. Pellicciotti, P. Burlando, B. Brock, and M. Funk, “Spatial and temporal variability of meteorological variables at Haut Glacier d’Arolla (Switzerland) during the ablation season 2001: Measurements and simulations,” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 109, no. D3. American Geophysical Union, 2004.","short":"U. Strasser, J. Corripio, F. Pellicciotti, P. Burlando, B. Brock, M. Funk, Journal of Geophysical Research: Atmospheres 109 (2004).","ista":"Strasser U, Corripio J, Pellicciotti F, Burlando P, Brock B, Funk M. 2004. Spatial and temporal variability of meteorological variables at Haut Glacier d’Arolla (Switzerland) during the ablation season 2001: Measurements and simulations. Journal of Geophysical Research: Atmospheres. 109(D3), D03103.","ama":"Strasser U, Corripio J, Pellicciotti F, Burlando P, Brock B, Funk M. Spatial and temporal variability of meteorological variables at Haut Glacier d’Arolla (Switzerland) during the ablation season 2001: Measurements and simulations. <i>Journal of Geophysical Research: Atmospheres</i>. 2004;109(D3). doi:<a href=\"https://doi.org/10.1029/2003jd003973\">10.1029/2003jd003973</a>"},"publication":"Journal of Geophysical Research: Atmospheres","publication_status":"published","abstract":[{"text":"[1] During the ablation period 2001 a glaciometeorological experiment was carried out on Haut Glacier d'Arolla, Switzerland. Five meteorological stations were installed on the glacier, and one permanent automatic weather station in the glacier foreland. The altitudes of the stations ranged between 2500 and 3000 m a.s.l., and they were in operation from end of May to beginning of September 2001. The spatial arrangement of the stations and temporal duration of the measurements generated a unique data set enabling the analysis of the spatial and temporal variability of the meteorological variables across an alpine glacier. All measurements were taken at a nominal height of 2 m, and hourly averages were derived for the analysis. The wind regime was dominated by the glacier wind (mean value 2.8 m s−1) but due to erosion by the synoptic gradient wind, occasionally the wind would blow up the valley. A slight decrease in mean 2 m air temperatures with altitude was found, however the 2 m air temperature gradient varied greatly and frequently changed its sign. Mean relative humidity was 71% and exhibited limited spatial variation. Mean incoming shortwave radiation and albedo both generally increased with elevation. The different components of shortwave radiation are quantified with a parameterization scheme. Resulting spatial variations are mainly due to horizon obstruction and reflections from surrounding slopes, i.e., topography. The effect of clouds accounts for a loss of 30% of the extraterrestrial flux. Albedos derived from a Landsat TM image of 30 July show remarkably constant values, in the range 0.49 to 0.50, across snow covered parts of the glacier, while albedo is highly spatially variable below the zone of continuous snow cover. These results are verified with ground measurements and compared with parameterized albedo. Mean longwave radiative fluxes decreased with elevation due to lower air temperatures and the effect of upper hemisphere slopes. It is shown through parameterization that this effect would even be more pronounced without the effect of clouds. Results are discussed with respect to a similar study which has been carried out on Pasterze Glacier (Austria). The presented algorithms for interpolating, parameterizing and simulating variables and parameters in alpine regions are integrated in the software package AMUNDSEN which is freely available to be adapted and further developed by the community.","lang":"eng"}],"article_number":"D03103","extern":"1","date_created":"2023-02-20T08:18:57Z","intvolume":"       109","volume":109,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"year":"2004","publication":"Structure","title":"Probing the energy landscape of the membrane protein bacteriorhodopsin","status":"public","publisher":"Cell Press","doi":"10.1016/j.str.2004.03.016","citation":{"ama":"Janovjak HL, Struckmeier J, Hubain M, Kessler M, Kedrov A, Mueller D. Probing the energy landscape of the membrane protein bacteriorhodopsin. <i>Structure</i>. 2004;12(5):871-879. doi:<a href=\"https://doi.org/10.1016/j.str.2004.03.016\">10.1016/j.str.2004.03.016</a>","ista":"Janovjak HL, Struckmeier J, Hubain M, Kessler M, Kedrov A, Mueller D. 2004. Probing the energy landscape of the membrane protein bacteriorhodopsin. Structure. 12(5), 871–879.","short":"H.L. Janovjak, J. Struckmeier, M. Hubain, M. Kessler, A. Kedrov, D. Mueller, Structure 12 (2004) 871–879.","chicago":"Janovjak, Harald L, Jens Struckmeier, Maurice Hubain, Max Kessler, Alexej Kedrov, and Daniel Mueller. “Probing the Energy Landscape of the Membrane Protein Bacteriorhodopsin.” <i>Structure</i>. Cell Press, 2004. <a href=\"https://doi.org/10.1016/j.str.2004.03.016\">https://doi.org/10.1016/j.str.2004.03.016</a>.","mla":"Janovjak, Harald L., et al. “Probing the Energy Landscape of the Membrane Protein Bacteriorhodopsin.” <i>Structure</i>, vol. 12, no. 5, Cell Press, 2004, pp. 871–79, doi:<a href=\"https://doi.org/10.1016/j.str.2004.03.016\">10.1016/j.str.2004.03.016</a>.","ieee":"H. L. Janovjak, J. Struckmeier, M. Hubain, M. Kessler, A. Kedrov, and D. Mueller, “Probing the energy landscape of the membrane protein bacteriorhodopsin,” <i>Structure</i>, vol. 12, no. 5. Cell Press, pp. 871–879, 2004.","apa":"Janovjak, H. L., Struckmeier, J., Hubain, M., Kessler, M., Kedrov, A., &#38; Mueller, D. (2004). Probing the energy landscape of the membrane protein bacteriorhodopsin. <i>Structure</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.str.2004.03.016\">https://doi.org/10.1016/j.str.2004.03.016</a>"},"publist_id":"2982","day":"01","type":"journal_article","author":[{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L","full_name":"Harald Janovjak","orcid":"0000-0002-8023-9315"},{"full_name":"Struckmeier, Jens","first_name":"Jens","last_name":"Struckmeier"},{"full_name":"Hubain, Maurice","first_name":"Maurice","last_name":"Hubain"},{"first_name":"Max","last_name":"Kessler","full_name":"Kessler, Max"},{"first_name":"Alexej","last_name":"Kedrov","full_name":"Kedrov, Alexej"},{"full_name":"Mueller, Daniel J","first_name":"Daniel","last_name":"Mueller"}],"date_updated":"2021-01-12T07:43:20Z","extern":1,"issue":"5","page":"871 - 879","intvolume":"        12","volume":12,"date_created":"2018-12-11T12:03:14Z","quality_controlled":0,"date_published":"2004-05-01T00:00:00Z","_id":"3419","month":"05","abstract":[{"lang":"eng","text":"The folding and stability of transmembrane proteins is a fundamental and unsolved biological problem. Here, single bacteriorhodopsin molecules were mechanically unfolded from native purple membranes using atomic force microscopy and force spectroscopy. The energy landscape of individual transmembrane α helices and polypeptide loops was mapped by monitoring the pulling speed dependence of the unfolding forces and applying Monte Carlo simulations. Single helices formed independently stable units stabilized by a single potential barrier. Mechanical unfolding of the helices was triggered by 3.9–7.7 Å extension, while natural unfolding rates were of the order of 10−3 s−1. Besides acting as individually stable units, helices associated pairwise, establishing a collective potential barrier. The unfolding pathways of individual proteins reflect distinct pulling speed-dependent unfolding routes in their energy landscapes. These observations support the two-stage model of membrane protein folding in which α helices insert into the membrane as stable units and then assemble into the functional protein."}],"publication_status":"published"},{"type":"journal_article","day":"23","author":[{"last_name":"Kedrov","first_name":"Alexej","full_name":"Kedrov, Alexej"},{"full_name":"Ziegler,  Christine","last_name":"Ziegler","first_name":"Christine"},{"full_name":"Harald Janovjak","last_name":"Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315"},{"first_name":"Werner","last_name":"Kühlbrandt","full_name":"Kühlbrandt, Werner"},{"full_name":"Mueller, Daniel J","first_name":"Daniel","last_name":"Mueller"}],"doi":"10.1016/j.jmb.2004.05.026","citation":{"apa":"Kedrov, A., Ziegler, C., Janovjak, H. L., Kühlbrandt, W., &#38; Mueller, D. (2004). Controlled unfolding and refolding of a single sodium/proton antiporter using atomic force microscopy. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2004.05.026\">https://doi.org/10.1016/j.jmb.2004.05.026</a>","ieee":"A. Kedrov, C. Ziegler, H. L. Janovjak, W. Kühlbrandt, and D. Mueller, “Controlled unfolding and refolding of a single sodium/proton antiporter using atomic force microscopy,” <i>Journal of Molecular Biology</i>, vol. 340, no. 5. Elsevier, pp. 1143–1152, 2004.","mla":"Kedrov, Alexej, et al. “Controlled Unfolding and Refolding of a Single Sodium/Proton Antiporter Using Atomic Force Microscopy.” <i>Journal of Molecular Biology</i>, vol. 340, no. 5, Elsevier, 2004, pp. 1143–52, doi:<a href=\"https://doi.org/10.1016/j.jmb.2004.05.026\">10.1016/j.jmb.2004.05.026</a>.","chicago":"Kedrov, Alexej, Christine Ziegler, Harald L Janovjak, Werner Kühlbrandt, and Daniel Mueller. “Controlled Unfolding and Refolding of a Single Sodium/Proton Antiporter Using Atomic Force Microscopy.” <i>Journal of Molecular Biology</i>. Elsevier, 2004. <a href=\"https://doi.org/10.1016/j.jmb.2004.05.026\">https://doi.org/10.1016/j.jmb.2004.05.026</a>.","short":"A. Kedrov, C. Ziegler, H.L. Janovjak, W. Kühlbrandt, D. Mueller, Journal of Molecular Biology 340 (2004) 1143–1152.","ista":"Kedrov A, Ziegler C, Janovjak HL, Kühlbrandt W, Mueller D. 2004. Controlled unfolding and refolding of a single sodium/proton antiporter using atomic force microscopy. Journal of Molecular Biology. 340(5), 1143–1152.","ama":"Kedrov A, Ziegler C, Janovjak HL, Kühlbrandt W, Mueller D. Controlled unfolding and refolding of a single sodium/proton antiporter using atomic force microscopy. <i>Journal of Molecular Biology</i>. 2004;340(5):1143-1152. doi:<a href=\"https://doi.org/10.1016/j.jmb.2004.05.026\">10.1016/j.jmb.2004.05.026</a>"},"publisher":"Elsevier","title":"Controlled unfolding and refolding of a single sodium/proton antiporter using atomic force microscopy","year":"2004","status":"public","publication":"Journal of Molecular Biology","publist_id":"2981","abstract":[{"lang":"eng","text":"Single-molecule force-spectroscopy was employed to unfold and refold single sodium-proton antiporters (NhaA) of Escherichia coli from membrane patches. Although transmembrane α-helices and extracellular polypeptide loops exhibited sufficient stability to individually establish potential barriers against unfolding, two helices predominantly unfolded pairwise, thereby acting as one structural unit. Many of the potential barriers were detected unfolding NhaA either from the C-terminal or the N-terminal end. It was found that some molecular interactions stabilizing secondary structural elements were directional, while others were not. Additionally, some interactions appeared to occur between the secondary structural elements. After unfolding ten of the 12 helices, the extracted polypeptide was allowed to refold back into the membrane. After five seconds, the refolded polypeptide established all secondary structure elements of the native protein. One helical pair showed a characteristic spring like “snap in” into its folded conformation, while the refolding process of other helices was not detected in particular. Additionally, individual helices required characteristic periods of time to fold. Correlating these results with the primary structure of NhaA allowed us to obtain the first insights into how potential barriers establish and determine the folding kinetics of the secondary structure elements."}],"publication_status":"published","month":"07","_id":"3420","issue":"5","page":"1143 - 1152","extern":1,"date_updated":"2021-01-12T07:43:21Z","quality_controlled":0,"date_created":"2018-12-11T12:03:14Z","date_published":"2004-07-23T00:00:00Z","intvolume":"       340","volume":340},{"page":"1395 - 1412","extern":1,"date_updated":"2021-01-12T07:44:24Z","date_published":"2004-04-15T00:00:00Z","quality_controlled":0,"date_created":"2018-12-11T12:04:02Z","publication_status":"published","month":"04","_id":"3574","publisher":"CRC Press","citation":{"ista":"Edelsbrunner H. 2004.Biological applications of computational topology. In: Handbook of Discrete and Computational Geometry. , 1395–1412.","ama":"Edelsbrunner H. Biological applications of computational topology. In: <i>Handbook of Discrete and Computational Geometry</i>. CRC Press; 2004:1395-1412.","short":"H. Edelsbrunner, in:, Handbook of Discrete and Computational Geometry, CRC Press, 2004, pp. 1395–1412.","chicago":"Edelsbrunner, Herbert. “Biological Applications of Computational Topology.” In <i>Handbook of Discrete and Computational Geometry</i>, 1395–1412. CRC Press, 2004.","mla":"Edelsbrunner, Herbert. “Biological Applications of Computational Topology.” <i>Handbook of Discrete and Computational Geometry</i>, CRC Press, 2004, pp. 1395–412.","ieee":"H. Edelsbrunner, “Biological applications of computational topology,” in <i>Handbook of Discrete and Computational Geometry</i>, CRC Press, 2004, pp. 1395–1412.","apa":"Edelsbrunner, H. (2004). Biological applications of computational topology. In <i>Handbook of Discrete and Computational Geometry</i> (pp. 1395–1412). CRC Press."},"title":"Biological applications of computational topology","year":"2004","publication":"Handbook of Discrete and Computational Geometry","status":"public","publist_id":"2811","type":"book_chapter","day":"15","author":[{"orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Herbert Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"main_file_link":[{"url":"http://www.cs.duke.edu/~edels/Papers/2004-B-01-BiologicalApplicationsTopology.pdf","open_access":"0"}]},{"date_published":"2004-01-01T00:00:00Z","date_created":"2018-12-11T12:04:02Z","quality_controlled":0,"intvolume":"       312","volume":312,"extern":1,"page":"37 - 57","date_updated":"2021-01-12T07:44:24Z","publication_status":"published","month":"01","abstract":[{"text":"The Jacobi set of two Morse functions defined on a common - manifold is the set of critical points of the restrictions of one func- tion to the level sets of the other function. Equivalently, it is the set of points where the gradients of the functions are parallel. For a generic pair of Morse functions, the Jacobi set is a smoothly embed- ded 1-manifold. We give a polynomial-time algorithm that com- putes the piecewise linear analog of the Jacobi set for functions specified at the vertices of a triangulation, and we generalize all results to more than two but at most Morse functions.","lang":"eng"}],"_id":"3575","publist_id":"2810","citation":{"mla":"Edelsbrunner, Herbert, and John Harer. “Jacobi Sets of Multiple Morse Functions.” <i>Foundations of Computational Mathematics</i>, vol. 312, Springer, 2004, pp. 37–57, doi:<a href=\"https://doi.org/10.1017/CBO9781139106962.003\">10.1017/CBO9781139106962.003</a>.","chicago":"Edelsbrunner, Herbert, and John Harer. “Jacobi Sets of Multiple Morse Functions.” In <i>Foundations of Computational Mathematics</i>, 312:37–57. Springer, 2004. <a href=\"https://doi.org/10.1017/CBO9781139106962.003\">https://doi.org/10.1017/CBO9781139106962.003</a>.","apa":"Edelsbrunner, H., &#38; Harer, J. (2004). Jacobi sets of multiple Morse functions. In <i>Foundations of Computational Mathematics</i> (Vol. 312, pp. 37–57). Springer. <a href=\"https://doi.org/10.1017/CBO9781139106962.003\">https://doi.org/10.1017/CBO9781139106962.003</a>","ieee":"H. Edelsbrunner and J. Harer, “Jacobi sets of multiple Morse functions,” in <i>Foundations of Computational Mathematics</i>, vol. 312, Springer, 2004, pp. 37–57.","short":"H. Edelsbrunner, J. Harer, in:, Foundations of Computational Mathematics, Springer, 2004, pp. 37–57.","ista":"Edelsbrunner H, Harer J. 2004.Jacobi sets of multiple Morse functions. In: Foundations of Computational Mathematics. London Mathematical Society Lecture Note, vol. 312, 37–57.","ama":"Edelsbrunner H, Harer J. Jacobi sets of multiple Morse functions. In: <i>Foundations of Computational Mathematics</i>. Vol 312. Springer; 2004:37-57. doi:<a href=\"https://doi.org/10.1017/CBO9781139106962.003\">10.1017/CBO9781139106962.003</a>"},"doi":"10.1017/CBO9781139106962.003","publisher":"Springer","title":"Jacobi sets of multiple Morse functions","status":"public","publication":"Foundations of Computational Mathematics","year":"2004","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Herbert Edelsbrunner","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833"},{"full_name":"Harer, John","first_name":"John","last_name":"Harer"}],"type":"book_chapter","alternative_title":["London Mathematical Society Lecture Note"],"day":"01"},{"editor":[{"full_name":"Korzh, Vladimir","first_name":"Vladimir","last_name":"Korzh"},{"full_name":"Gong, Zhiyuan","last_name":"Gong","first_name":"Zhiyuan"}],"publication_status":"published","month":"11","article_processing_charge":"No","_id":"3587","date_published":"2004-11-01T00:00:00Z","date_created":"2018-12-11T12:04:06Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":2,"intvolume":"         2","language":[{"iso":"eng"}],"page":"39 - 86","extern":"1","date_updated":"2021-01-12T07:44:29Z","author":[{"last_name":"Ulrich","first_name":"Florian","full_name":"Ulrich, Florian"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"type":"book_chapter","alternative_title":["Molecular Aspects of Fish and Marine Biology"],"day":"01","oa_version":"None","publist_id":"2796","citation":{"ama":"Ulrich F, Heisenberg C-PJ. Gastrulation in zebrafish. In: Korzh V, Gong Z, eds. <i>Fish Development and Genetics : The Zebrafish and Medaka Models</i>. Vol 2. World Scientific Publishing; 2004:39-86.","ista":"Ulrich F, Heisenberg C-PJ. 2004.Gastrulation in zebrafish. In: Fish development and genetics : the zebrafish and medaka models. Molecular Aspects of Fish and Marine Biology, vol. 2, 39–86.","short":"F. Ulrich, C.-P.J. Heisenberg, in:, V. Korzh, Z. Gong (Eds.), Fish Development and Genetics : The Zebrafish and Medaka Models, World Scientific Publishing, 2004, pp. 39–86.","chicago":"Ulrich, Florian, and Carl-Philipp J Heisenberg. “Gastrulation in Zebrafish.” In <i>Fish Development and Genetics : The Zebrafish and Medaka Models</i>, edited by Vladimir Korzh and Zhiyuan Gong, 2:39–86. World Scientific Publishing, 2004.","mla":"Ulrich, Florian, and Carl-Philipp J. Heisenberg. “Gastrulation in Zebrafish.” <i>Fish Development and Genetics : The Zebrafish and Medaka Models</i>, edited by Vladimir Korzh and Zhiyuan Gong, vol. 2, World Scientific Publishing, 2004, pp. 39–86.","ieee":"F. Ulrich and C.-P. J. Heisenberg, “Gastrulation in zebrafish,” in <i>Fish development and genetics : the zebrafish and medaka models</i>, vol. 2, V. Korzh and Z. Gong, Eds. World Scientific Publishing, 2004, pp. 39–86.","apa":"Ulrich, F., &#38; Heisenberg, C.-P. J. (2004). Gastrulation in zebrafish. In V. Korzh &#38; Z. Gong (Eds.), <i>Fish development and genetics : the zebrafish and medaka models</i> (Vol. 2, pp. 39–86). World Scientific Publishing."},"publisher":"World Scientific Publishing","title":"Gastrulation in zebrafish","publication":"Fish development and genetics : the zebrafish and medaka models","status":"public","year":"2004"},{"citation":{"short":"B. Charlesworth, N.H. Barton, Current Biology 14 (2004) R233–R235.","ista":"Charlesworth B, Barton NH. 2004. Genome size: Does bigger mean worse? Current Biology. 14(6), R233–R235.","ama":"Charlesworth B, Barton NH. Genome size: Does bigger mean worse? <i>Current Biology</i>. 2004;14(6):R233-R235. doi:<a href=\"https://doi.org/10.1016/j.cub.2004.02.054\">10.1016/j.cub.2004.02.054</a>","mla":"Charlesworth, Brian, and Nicholas H. Barton. “Genome Size: Does Bigger Mean Worse?” <i>Current Biology</i>, vol. 14, no. 6, Cell Press, 2004, pp. R233–35, doi:<a href=\"https://doi.org/10.1016/j.cub.2004.02.054\">10.1016/j.cub.2004.02.054</a>.","chicago":"Charlesworth, Brian, and Nicholas H Barton. “Genome Size: Does Bigger Mean Worse?” <i>Current Biology</i>. Cell Press, 2004. <a href=\"https://doi.org/10.1016/j.cub.2004.02.054\">https://doi.org/10.1016/j.cub.2004.02.054</a>.","apa":"Charlesworth, B., &#38; Barton, N. H. (2004). Genome size: Does bigger mean worse? <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2004.02.054\">https://doi.org/10.1016/j.cub.2004.02.054</a>","ieee":"B. Charlesworth and N. H. Barton, “Genome size: Does bigger mean worse?,” <i>Current Biology</i>, vol. 14, no. 6. Cell Press, pp. R233–R235, 2004."},"doi":"10.1016/j.cub.2004.02.054","publisher":"Cell Press","title":"Genome size: Does bigger mean worse?","year":"2004","publication":"Current Biology","status":"public","publist_id":"2788","type":"review","day":"01","author":[{"first_name":"Brian","last_name":"Charlesworth","full_name":"Charlesworth, Brian"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Nicholas Barton","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"page":"R233 - R235","extern":1,"issue":"6","date_updated":"2019-04-26T07:22:31Z","date_published":"2004-03-01T00:00:00Z","quality_controlled":0,"date_created":"2018-12-11T12:04:09Z","intvolume":"        14","volume":14,"publication_status":"published","month":"03","abstract":[{"text":"Genome sizes vary enormously. This variation in DNA content correlates with effective population size, suggesting that deleterious additions to the genome can accumulate in small populations. On this view, the increased complexity of biological functions associated with large genomes partly reflects evolutionary degeneration.","lang":"eng"}],"_id":"3595"}]