[{"publisher":"Cold Spring Harbor Laboratory Press","date_updated":"2021-01-12T08:21:47Z","publication_status":"published","day":"01","quality_controlled":0,"title":"The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint","doi":"10.1101/gr.2195604","volume":14,"type":"journal_article","year":"2004","date_created":"2018-12-11T11:49:06Z","citation":{"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>","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.","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>","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>.","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>.","short":"C. Castillo Davis, F. Kondrashov, D. Hartl, R. Kulathinal, Genome Research 14 (2004) 802–811."},"extern":1,"month":"05","author":[{"first_name":"Cristian","last_name":"Castillo Davis","full_name":"Castillo-Davis, Cristian I"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694"},{"full_name":"Hartl, Daniel L","last_name":"Hartl","first_name":"Daniel"},{"last_name":"Kulathinal","first_name":"Rob","full_name":"Kulathinal, Rob J"}],"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.","intvolume":"        14","_id":"902","status":"public","date_published":"2004-05-01T00:00:00Z","publist_id":"6750","issue":"5","publication":"Genome Research","abstract":[{"lang":"eng","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."}],"page":"802 - 811"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7333","intvolume":"         4","language":[{"iso":"eng"}],"abstract":[{"text":"The analysis of the complete H2/air polymer electrolyte fuel cell system shows that process air humidification is one of the biggest obstacles for a high performance portable system in the kW range. Therefore, a new concept, with passive process air humidification integrated into the stack, has been developed. Humidification in each cell makes the process independent from the number of cells and the operation mode, thus making the concept fully scalable. Without external humidification the system is simpler, smaller, and cheaper. The humidification of the process air is achieved by transfer of product water from the exhaust air, through part of the membrane, to the dry intake air. Tests have shown that cells using the concept of internal humidification and operated with dry air at 70 ° have almost the same performance as when operated with external humidification. A 42‐cell stack with this internal humidification concept was built and integrated into a portable 1 kW power generator system.","lang":"eng"}],"page":"214-218","date_published":"2004-08-01T00:00:00Z","status":"public","issue":"3","publication":"Fuel Cells","article_type":"original","extern":"1","date_created":"2020-01-15T12:24:14Z","citation":{"mla":"Santis, M., et al. “Modular Stack-Internal Air Humidification Concept-Verification in a 1 KW Stack.” <i>Fuel Cells</i>, vol. 4, no. 3, Wiley, 2004, pp. 214–18, doi:<a href=\"https://doi.org/10.1002/fuce.200400028\">10.1002/fuce.200400028</a>.","short":"M. Santis, D. Schmid, M. Ruge, S.A. Freunberger, F.N. Büchi, Fuel Cells 4 (2004) 214–218.","chicago":"Santis, M., D. Schmid, M. Ruge, Stefan Alexander Freunberger, and F.N. Büchi. “Modular Stack-Internal Air Humidification Concept-Verification in a 1 KW Stack.” <i>Fuel Cells</i>. Wiley, 2004. <a href=\"https://doi.org/10.1002/fuce.200400028\">https://doi.org/10.1002/fuce.200400028</a>.","ieee":"M. Santis, D. Schmid, M. Ruge, S. A. Freunberger, and F. N. Büchi, “Modular stack-internal air humidification concept-verification in a 1 kW stack,” <i>Fuel Cells</i>, vol. 4, no. 3. Wiley, pp. 214–218, 2004.","ista":"Santis M, Schmid D, Ruge M, Freunberger SA, Büchi FN. 2004. Modular stack-internal air humidification concept-verification in a 1 kW stack. Fuel Cells. 4(3), 214–218.","apa":"Santis, M., Schmid, D., Ruge, M., Freunberger, S. A., &#38; Büchi, F. N. (2004). Modular stack-internal air humidification concept-verification in a 1 kW stack. <i>Fuel Cells</i>. Wiley. <a href=\"https://doi.org/10.1002/fuce.200400028\">https://doi.org/10.1002/fuce.200400028</a>","ama":"Santis M, Schmid D, Ruge M, Freunberger SA, Büchi FN. Modular stack-internal air humidification concept-verification in a 1 kW stack. <i>Fuel Cells</i>. 2004;4(3):214-218. doi:<a href=\"https://doi.org/10.1002/fuce.200400028\">10.1002/fuce.200400028</a>"},"month":"08","author":[{"full_name":"Santis, M.","first_name":"M.","last_name":"Santis"},{"full_name":"Schmid, D.","first_name":"D.","last_name":"Schmid"},{"first_name":"M.","last_name":"Ruge","full_name":"Ruge, M."},{"orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","first_name":"Stefan Alexander"},{"full_name":"Büchi, F.N.","last_name":"Büchi","first_name":"F.N."}],"oa_version":"None","volume":4,"type":"journal_article","article_processing_charge":"No","year":"2004","publication_identifier":{"issn":["1615-6846","1615-6854"]},"publication_status":"published","day":"01","publisher":"Wiley","date_updated":"2021-01-12T08:13:08Z","title":"Modular stack-internal air humidification concept-verification in a 1 kW stack","doi":"10.1002/fuce.200400028","quality_controlled":"1"},{"author":[{"full_name":"Mantzaras, John","first_name":"John","last_name":"Mantzaras"},{"full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","first_name":"Stefan Alexander"},{"full_name":"Büchi, Felix N.","first_name":"Felix N.","last_name":"Büchi"},{"last_name":"Roos","first_name":"Markus","full_name":"Roos, Markus"},{"last_name":"Brandstätter","first_name":"Wilhelm","full_name":"Brandstätter, Wilhelm"},{"full_name":"Prestat, Michel","first_name":"Michel","last_name":"Prestat"},{"first_name":"Ludwig J.","last_name":"Gauckler","full_name":"Gauckler, Ludwig J."},{"last_name":"Andreaus","first_name":"Bernhard","full_name":"Andreaus, Bernhard"},{"first_name":"Faegheh","last_name":"Hajbolouri","full_name":"Hajbolouri, Faegheh"},{"first_name":"Stephan M.","last_name":"Senn","full_name":"Senn, Stephan M."},{"first_name":"Dimos","last_name":"Poulikakos","full_name":"Poulikakos, Dimos"},{"last_name":"Chaniotis","first_name":"Andreas K.","full_name":"Chaniotis, Andreas K."},{"first_name":"Diego","last_name":"Larrain","full_name":"Larrain, Diego"},{"full_name":"Autissier, Nordahl","last_name":"Autissier","first_name":"Nordahl"},{"first_name":"François","last_name":"Maréchal","full_name":"Maréchal, François"}],"oa_version":"None","month":"12","article_type":"original","extern":"1","citation":{"ama":"Mantzaras J, Freunberger SA, Büchi FN, et al. Fuel cell modeling and simulations. <i>CHIMIA International Journal for Chemistry</i>. 2004;58(12):857-868. doi:<a href=\"https://doi.org/10.2533/000942904777677029\">10.2533/000942904777677029</a>","apa":"Mantzaras, J., Freunberger, S. A., Büchi, F. N., Roos, M., Brandstätter, W., Prestat, M., … Maréchal, F. (2004). Fuel cell modeling and simulations. <i>CHIMIA International Journal for Chemistry</i>. Swiss Chemical Society. <a href=\"https://doi.org/10.2533/000942904777677029\">https://doi.org/10.2533/000942904777677029</a>","ista":"Mantzaras J, Freunberger SA, Büchi FN, Roos M, Brandstätter W, Prestat M, Gauckler LJ, Andreaus B, Hajbolouri F, Senn SM, Poulikakos D, Chaniotis AK, Larrain D, Autissier N, Maréchal F. 2004. Fuel cell modeling and simulations. CHIMIA International Journal for Chemistry. 58(12), 857–868.","ieee":"J. Mantzaras <i>et al.</i>, “Fuel cell modeling and simulations,” <i>CHIMIA International Journal for Chemistry</i>, vol. 58, no. 12. Swiss Chemical Society, pp. 857–868, 2004.","chicago":"Mantzaras, John, Stefan Alexander Freunberger, Felix N. Büchi, Markus Roos, Wilhelm Brandstätter, Michel Prestat, Ludwig J. Gauckler, et al. “Fuel Cell Modeling and Simulations.” <i>CHIMIA International Journal for Chemistry</i>. Swiss Chemical Society, 2004. <a href=\"https://doi.org/10.2533/000942904777677029\">https://doi.org/10.2533/000942904777677029</a>.","mla":"Mantzaras, John, et al. “Fuel Cell Modeling and Simulations.” <i>CHIMIA International Journal for Chemistry</i>, vol. 58, no. 12, Swiss Chemical Society, 2004, pp. 857–68, doi:<a href=\"https://doi.org/10.2533/000942904777677029\">10.2533/000942904777677029</a>.","short":"J. Mantzaras, S.A. Freunberger, F.N. Büchi, M. Roos, W. Brandstätter, M. Prestat, L.J. Gauckler, B. Andreaus, F. Hajbolouri, S.M. Senn, D. Poulikakos, A.K. Chaniotis, D. Larrain, N. Autissier, F. Maréchal, CHIMIA International Journal for Chemistry 58 (2004) 857–868."},"date_created":"2020-01-15T12:24:23Z","page":"857-868","abstract":[{"lang":"eng","text":"Fundamental and phenomenological models for cells, stacks, and complete systems of PEFC and SOFC are reviewed and their predictive power is assessed by comparing model simulations against experiments. Computationally efficient models suited for engineering design include the (1+1) dimensionality approach, which decouples the membrane in-plane and through-plane processes, and the volume-averaged-method (VAM) that considers only the lumped effect of pre-selected system components. The former model was shown to capture the measured lateral current density inhomogeneities in a PEFC and the latter was used for the optimization of commercial SOFC systems. State Space Modeling (SSM) was used to identify the main reaction pathways in SOFC and, in conjunction with the implementation of geometrically well-defined electrodes, has opened a new direction for the understanding of electrochemical reactions. Furthermore, SSM has advanced the understanding of the COpoisoning-induced anode impedance in PEFC. Detailed numerical models such as the Lattice Boltzmann (LB) method for transport in porous media and the full 3-D Computational Fluid Dynamics (CFD) Navier-Stokes simulations are addressed. These models contain all components of the relevant physics and they can improve the understanding of the related phenomena, a necessary condition for the development of both appropriate simplified models as well as reliable technologies. Within the LB framework, a technique for the characterization and computer-reconstruction of the porous electrode structure was developed using advanced pattern recognition algorithms. In CFD modeling, 3-D simulations were used to investigate SOFC with internal methane steam reforming and have exemplified the significance of porous and novel fractal channel distributors for the fuel and oxidant delivery, as well as for the cooling of PEFC. As importantly, the novel concept has been put forth of functionally designed, fractal-shaped fuel cells, showing promise of significant performance improvements over the conventional rectangular shaped units. Thermo-economic modeling for the optimization of PEFC is finally addressed. "}],"publication":"CHIMIA International Journal for Chemistry","issue":"12","date_published":"2004-12-01T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        58","_id":"7334","language":[{"iso":"eng"}],"doi":"10.2533/000942904777677029","title":"Fuel cell modeling and simulations","quality_controlled":"1","day":"01","publication_identifier":{"issn":["0009-4293"]},"publication_status":"published","date_updated":"2021-01-12T08:13:09Z","publisher":"Swiss Chemical Society","year":"2004","type":"journal_article","volume":58,"article_processing_charge":"No"},{"article_processing_charge":"No","volume":303,"type":"journal_article","year":"2004","publisher":"American Association for the Advancement of Science","date_updated":"2024-01-31T10:14:17Z","publication_identifier":{"issn":["0036-8075","1095-9203"]},"publication_status":"published","day":"26","quality_controlled":"1","title":"Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase","doi":"10.1126/science.1094637","_id":"7706","intvolume":"       303","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2004-03-26T00:00:00Z","publication":"Science","issue":"5666","abstract":[{"text":"The Sir2 deacetylase modulates organismal life-span in various species. However, the molecular mechanisms by which Sir2 increases longevity are largely unknown. We show that in mammalian cells, the Sir2 homolog SIRT1 appears to control the cellular response to stress by regulating the FOXO family of Forkhead transcription factors, a family of proteins that function as sensors of the insulin signaling pathway and as regulators of organismal longevity. SIRT1 and the FOXO transcription factor FOXO3 formed a complex in cells in response to oxidative stress, and SIRT1 deacetylated FOXO3 in vitro and within cells. SIRT1 had a dual effect on FOXO3 function: SIRT1 increased FOXO3's ability to induce cell cycle arrest and resistance to oxidative stress but inhibited FOXO3's ability to induce cell death. Thus, one way in which members of the Sir2 family of proteins may increase organismal longevity is by tipping FOXO-dependent responses away from apoptosis and toward stress resistance.","lang":"eng"}],"page":"2011-2015","citation":{"chicago":"Brunet, Anne, Lora B. Sweeney, J Fitzhugh  Sturgill, Katrin Chua, Paul Greer, Yingxi Lin, Hien Tran, et al. “Stress-Dependent Regulation of FOXO Transcription Factors by the SIRT1 Deacetylase.” <i>Science</i>. American Association for the Advancement of Science, 2004. <a href=\"https://doi.org/10.1126/science.1094637\">https://doi.org/10.1126/science.1094637</a>.","ieee":"A. Brunet <i>et al.</i>, “Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase,” <i>Science</i>, vol. 303, no. 5666. American Association for the Advancement of Science, pp. 2011–2015, 2004.","short":"A. Brunet, L.B. Sweeney, J.F. Sturgill, K. Chua, P. Greer, Y. Lin, H. Tran, S. Ross, R. Mostoslavsky, H. Cohen, L. Hu, H.-L. Chen, M. Jedrychowski, S. Gygi, D. Sinclair, F. Alt, M. Greenberg, Science 303 (2004) 2011–2015.","mla":"Brunet, Anne, et al. “Stress-Dependent Regulation of FOXO Transcription Factors by the SIRT1 Deacetylase.” <i>Science</i>, vol. 303, no. 5666, American Association for the Advancement of Science, 2004, pp. 2011–15, doi:<a href=\"https://doi.org/10.1126/science.1094637\">10.1126/science.1094637</a>.","ama":"Brunet A, Sweeney LB, Sturgill JF, et al. Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase. <i>Science</i>. 2004;303(5666):2011-2015. doi:<a href=\"https://doi.org/10.1126/science.1094637\">10.1126/science.1094637</a>","ista":"Brunet A, Sweeney LB, Sturgill JF, Chua K, Greer P, Lin Y, Tran H, Ross S, Mostoslavsky R, Cohen H, Hu L, Chen H-L, Jedrychowski M, Gygi S, Sinclair D, Alt F, Greenberg M. 2004. Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase. Science. 303(5666), 2011–2015.","apa":"Brunet, A., Sweeney, L. B., Sturgill, J. F., Chua, K., Greer, P., Lin, Y., … Greenberg, M. (2004). Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1094637\">https://doi.org/10.1126/science.1094637</a>"},"date_created":"2020-04-30T10:37:41Z","article_type":"original","extern":"1","month":"03","author":[{"full_name":"Brunet, Anne","last_name":"Brunet","first_name":"Anne"},{"id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","first_name":"Lora Beatrice Jaeger","last_name":"Sweeney","orcid":"0000-0001-9242-5601","full_name":"Sweeney, Lora Beatrice Jaeger"},{"first_name":"J Fitzhugh ","last_name":"Sturgill","full_name":"Sturgill, J Fitzhugh "},{"first_name":"Katrin","last_name":"Chua","full_name":"Chua, Katrin"},{"full_name":"Greer, Paul","first_name":"Paul","last_name":"Greer"},{"last_name":"Lin","first_name":"Yingxi","full_name":"Lin, Yingxi"},{"last_name":"Tran","first_name":"Hien","full_name":"Tran, Hien"},{"full_name":"Ross, Sarah","first_name":"Sarah","last_name":"Ross"},{"full_name":"Mostoslavsky, Raul","last_name":"Mostoslavsky","first_name":"Raul"},{"full_name":"Cohen, Haim","first_name":"Haim","last_name":"Cohen"},{"full_name":"Hu, Linda","last_name":"Hu","first_name":"Linda"},{"full_name":"Chen, Hwei-Ling","first_name":"Hwei-Ling","last_name":"Chen"},{"last_name":"Jedrychowski","first_name":"Mark","full_name":"Jedrychowski, Mark"},{"full_name":"Gygi, Steven","first_name":"Steven","last_name":"Gygi"},{"full_name":"Sinclair, David","first_name":"David","last_name":"Sinclair"},{"first_name":"Frederick","last_name":"Alt","full_name":"Alt, Frederick"},{"full_name":"Greenberg, Michael","last_name":"Greenberg","first_name":"Michael"}],"oa_version":"None"},{"month":"05","author":[{"full_name":"Mamedova, Aygun A","last_name":"Mamedova","first_name":"Aygun"},{"first_name":"Peter","last_name":"Holt","full_name":"Holt, Peter J"},{"last_name":"Carroll","first_name":"Joe","full_name":"Carroll, Joe D"},{"orcid":"0000-0002-0977-7989","full_name":"Leonid Sazanov","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"citation":{"mla":"Mamedova, Aygun, et al. “Substrate-Induced Conformational Change in Bacterial Complex I.” <i>Journal of Biological Chemistry</i>, vol. 279, no. 22, American Society for Biochemistry and Molecular Biology, 2004, pp. 23830–36, doi:<a href=\"https://doi.org/10.1074/jbc.M401539200\">10.1074/jbc.M401539200</a>.","short":"A. Mamedova, P. Holt, J. Carroll, L.A. Sazanov, Journal of Biological Chemistry 279 (2004) 23830–23836.","chicago":"Mamedova, Aygun, Peter Holt, Joe Carroll, and Leonid A Sazanov. “Substrate-Induced Conformational Change in Bacterial Complex I.” <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology, 2004. <a href=\"https://doi.org/10.1074/jbc.M401539200\">https://doi.org/10.1074/jbc.M401539200</a>.","ieee":"A. Mamedova, P. Holt, J. Carroll, and L. A. Sazanov, “Substrate-induced conformational change in bacterial complex I,” <i>Journal of Biological Chemistry</i>, vol. 279, no. 22. American Society for Biochemistry and Molecular Biology, pp. 23830–23836, 2004.","ista":"Mamedova A, Holt P, Carroll J, Sazanov LA. 2004. Substrate-induced conformational change in bacterial complex I. Journal of Biological Chemistry. 279(22), 23830–23836.","apa":"Mamedova, A., Holt, P., Carroll, J., &#38; Sazanov, L. A. (2004). Substrate-induced conformational change in bacterial complex I. <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology. <a href=\"https://doi.org/10.1074/jbc.M401539200\">https://doi.org/10.1074/jbc.M401539200</a>","ama":"Mamedova A, Holt P, Carroll J, Sazanov LA. Substrate-induced conformational change in bacterial complex I. <i>Journal of Biological Chemistry</i>. 2004;279(22):23830-23836. doi:<a href=\"https://doi.org/10.1074/jbc.M401539200\">10.1074/jbc.M401539200</a>"},"date_created":"2018-12-11T11:54:56Z","extern":1,"status":"public","date_published":"2004-05-28T00:00:00Z","issue":"22","publist_id":"5123","publication":"Journal of Biological Chemistry","abstract":[{"text":"The mechanism coupling electron transfer and proton pumping in respiratory complex I (NADH-ubiquinone oxidoreductase) has not been established, but it has been suggested that it involves conformational changes. Here, the influence of substrates on the conformation of purified complex I from Escherichia coli was studied by cross-linking and electron microscopy. When a zero-length cross-linking reagent was used, the presence of NAD(P)H, in contrast to that of NAD+, prevented the formation of cross-links between the hydrophilic subunits of the complex, including NuoB, NuoI, and NuoCD. Comparisons using different cross-linkers suggested that NuoB, which is likely to coordinate the key iron-sulfur cluster N2, is the most mobile subunit. The presence of NAD(P)H led also to enhanced proteolysis of subunit NuoG. These data indicate that upon NAD(P)H binding, the peripheral arm of the complex adopts a more open conformation, with increased distances between subunits. Single particle analysis showed the nature of this conformational change. The enzyme retains its L-shape in the presence of NADH, but exhibits a significantly more open or expanded structure both in the peripheral arm and, unexpectedly, in the membrane domain also.","lang":"eng"}],"page":"23830 - 23836","acknowledgement":"This work was supported by the Medical Research Council and by a Royal Society/North Atlantic Treaty Organization postdoctoral fellowship (to A. A. M.)","intvolume":"       279","_id":"1963","quality_controlled":0,"title":"Substrate-induced conformational change in bacterial complex I","doi":"10.1074/jbc.M401539200","publisher":"American Society for Biochemistry and Molecular Biology","date_updated":"2021-01-12T06:54:22Z","publication_status":"published","day":"28","year":"2004","volume":279,"type":"journal_article"},{"article_processing_charge":"No","year":"2004","day":"14","publication_identifier":{"eissn":["1521-4095"],"issn":["0935-9648"]},"date_updated":"2023-08-08T12:41:23Z","doi":"10.1002/adma.200400383","title":"Color micro- and nanopatterning with counter-propagating reaction-diffusion fronts","_id":"13434","language":[{"iso":"eng"}],"page":"1912-1917","issue":"21","article_type":"original","keyword":["Mechanical Engineering","Mechanics of Materials","General Materials Science"],"citation":{"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.","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>.","short":"C.J. Campbell, M. Fialkowski, R. Klajn, I.T. Bensemann, B.A. Grzybowski, Advanced Materials 16 (2004) 1912–1917.","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>.","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>","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>","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."},"author":[{"first_name":"C. J.","last_name":"Campbell","full_name":"Campbell, C. J."},{"full_name":"Fialkowski, M.","last_name":"Fialkowski","first_name":"M."},{"last_name":"Klajn","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal"},{"last_name":"Bensemann","first_name":"I. T.","full_name":"Bensemann, I. T."},{"first_name":"B. A.","last_name":"Grzybowski","full_name":"Grzybowski, B. A."}],"month":"11","type":"journal_article","volume":16,"publication_status":"published","publisher":"Wiley","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        16","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."}],"publication":"Advanced Materials","status":"public","date_published":"2004-11-14T00:00:00Z","scopus_import":"1","extern":"1","date_created":"2023-08-01T10:39:09Z","oa_version":"None"},{"page":"729-735","_id":"13435","language":[{"iso":"eng"}],"month":"09","author":[{"full_name":"Klajn, Rafal","last_name":"Klajn","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"},{"first_name":"Marcin","last_name":"Fialkowski","full_name":"Fialkowski, Marcin"},{"last_name":"Bensemann","first_name":"Igor T.","full_name":"Bensemann, Igor T."},{"first_name":"Agnieszka","last_name":"Bitner","full_name":"Bitner, Agnieszka"},{"full_name":"Campbell, C. J.","last_name":"Campbell","first_name":"C. J."},{"first_name":"Kyle","last_name":"Bishop","full_name":"Bishop, Kyle"},{"last_name":"Smoukov","first_name":"Stoyan","full_name":"Smoukov, Stoyan"},{"first_name":"Bartosz A.","last_name":"Grzybowski","full_name":"Grzybowski, Bartosz A."}],"keyword":["Mechanical Engineering","Mechanics of Materials","Condensed Matter Physics","General Materials Science","General Chemistry"],"citation":{"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>","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.","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>","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>.","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.","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.","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>."},"article_type":"original","year":"2004","article_processing_charge":"No","external_id":{"pmid":["15378052"]},"title":"Multicolour micropatterning of thin films of dry gels","doi":"10.1038/nmat1231","date_updated":"2023-08-08T12:42:51Z","publication_identifier":{"issn":["1476-1122"],"eissn":["1476-4660"]},"day":"19","status":"public","date_published":"2004-09-19T00:00:00Z","publication":"Nature Materials","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"}],"intvolume":"         3","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","date_created":"2023-08-01T10:39:23Z","scopus_import":"1","extern":"1","volume":3,"type":"journal_article","pmid":1,"quality_controlled":"1","publisher":"Springer Nature","publication_status":"published"},{"issue":"3","publist_id":"5737","publication":"Duke Mathematical Journal","date_published":"2004-04-15T00:00:00Z","status":"public","page":"485 - 548","abstract":[{"text":"We study the space of L2 harmonic forms on complete manifolds with metrics of fibred boundary or fibred cusp type. These metrics generalize the geometric structures at infinity of several different well-known classes of metrics, including asymptotically locally Euclidean manifolds, the (known types of) gravitational instantons, and also Poincaré metrics on ℚ-rank 1 ends of locally symmetric spaces and on the complements of smooth divisors in Kähler manifolds. The answer in all cases is given in terms of intersection cohomology of a stratified compactification of the manifold. The L2 signature formula implied by our result is closely related to the one proved by Dai and more generally by Vaillant and identifies Dai's τ-invariant directly in terms of intersection cohomology of differing perversities. This work is also closely related to a recent paper of Carron and the forthcoming paper of Cheeger and Dai. We apply our results to a number of examples, gravitational instantons among them, arising in predictions about L2 harmonic forms in duality theories in string theory.","lang":"eng"}],"_id":"1456","intvolume":"       122","acknowledgement":"Hausel’s work supported by a Miller Research Fellowship at the University of California, Berkeley.\nHunsicker’s work partially supported by Stanford University.\nMazzeo’s work supported by National Science Foundation grant numbers DMS-991975 and DMS-0204730 and\nby the Mathematical Sciences Research Institute.","author":[{"full_name":"Tamas Hausel","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel","first_name":"Tamas"},{"last_name":"Hunsicker","first_name":"Eugénie","full_name":"Hunsicker, Eugénie"},{"full_name":"Mazzeo, Rafe R","first_name":"Rafe","last_name":"Mazzeo"}],"month":"04","citation":{"apa":"Hausel, T., Hunsicker, E., &#38; Mazzeo, R. (2004). Hodge cohomology of gravitational instantons. <i>Duke Mathematical Journal</i>. Duke University Press. <a href=\"https://doi.org/10.1215/S0012-7094-04-12233-X\">https://doi.org/10.1215/S0012-7094-04-12233-X</a>","ista":"Hausel T, Hunsicker E, Mazzeo R. 2004. Hodge cohomology of gravitational instantons. Duke Mathematical Journal. 122(3), 485–548.","ama":"Hausel T, Hunsicker E, Mazzeo R. Hodge cohomology of gravitational instantons. <i>Duke Mathematical Journal</i>. 2004;122(3):485-548. doi:<a href=\"https://doi.org/10.1215/S0012-7094-04-12233-X\">10.1215/S0012-7094-04-12233-X</a>","short":"T. Hausel, E. Hunsicker, R. Mazzeo, Duke Mathematical Journal 122 (2004) 485–548.","mla":"Hausel, Tamás, et al. “Hodge Cohomology of Gravitational Instantons.” <i>Duke Mathematical Journal</i>, vol. 122, no. 3, Duke University Press, 2004, pp. 485–548, doi:<a href=\"https://doi.org/10.1215/S0012-7094-04-12233-X\">10.1215/S0012-7094-04-12233-X</a>.","ieee":"T. Hausel, E. Hunsicker, and R. Mazzeo, “Hodge cohomology of gravitational instantons,” <i>Duke Mathematical Journal</i>, vol. 122, no. 3. Duke University Press, pp. 485–548, 2004.","chicago":"Hausel, Tamás, Eugénie Hunsicker, and Rafe Mazzeo. “Hodge Cohomology of Gravitational Instantons.” <i>Duke Mathematical Journal</i>. Duke University Press, 2004. <a href=\"https://doi.org/10.1215/S0012-7094-04-12233-X\">https://doi.org/10.1215/S0012-7094-04-12233-X</a>."},"date_created":"2018-12-11T11:52:08Z","extern":1,"main_file_link":[{"url":"http://arxiv.org/abs/math/0207169","open_access":"1"}],"year":"2004","oa":1,"type":"journal_article","volume":122,"quality_controlled":0,"doi":"10.1215/S0012-7094-04-12233-X","title":"Hodge cohomology of gravitational instantons","date_updated":"2021-01-12T06:50:52Z","publisher":"Duke University Press","day":"15","publication_status":"published"},{"date_created":"2018-12-11T11:52:10Z","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.","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>.","short":"T. Hausel, M. Thaddeus, Proceedings of the London Mathematical Society 88 (2004) 632–658.","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>","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>","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."},"extern":1,"month":"05","author":[{"full_name":"Tamas Hausel","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel","first_name":"Tamas"},{"full_name":"Thaddeus, Michael","last_name":"Thaddeus","first_name":"Michael"}],"intvolume":"        88","_id":"1464","date_published":"2004-05-01T00:00:00Z","status":"public","publication":"Proceedings of the London Mathematical Society","publist_id":"5736","issue":"3","abstract":[{"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). ","lang":"eng"}],"page":"632 - 658","publisher":"Oxford University Press","date_updated":"2021-01-12T06:50:55Z","publication_status":"published","day":"01","quality_controlled":0,"title":"Generators for the cohomology ring of the moduli space of rank 2 higgs bundles","doi":"10.1112/S0024611503014618","oa":1,"volume":88,"type":"journal_article","year":"2004","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/math/0003093"}]},{"_id":"6155","language":[{"iso":"eng"}],"intvolume":"        14","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication":"Current Biology","issue":"12","status":"public","date_published":"2004-06-22T00:00:00Z","page":"1105-1111","abstract":[{"text":"The genome of the nematode Caenorhabditis elegans encodes seven soluble guanylate cyclases (sGCs) [1]. In mammals, sGCs function as α/β heterodimers activated by gaseous ligands binding to a haem prosthetic group 2, 3. The principal activator is nitric oxide, which acts through sGCs to regulate diverse cellular events. In C. elegans the function of sGCs is mysterious: the worm genome does not appear to encode nitric oxide synthase, and all C. elegans sGC subunits are more closely related to mammalian β than α subunits [1]. Here, we show that two of the seven C. elegans sGCs, GCY-35 and GCY-36, promote aggregation behavior. gcy-35 and gcy-36 are expressed in a small number of neurons. These include the body cavity neurons AQR, PQR, and URX, which are directly exposed to the blood equivalent of C. elegans and regulate aggregation behavior [4]. We show that GCY-35 and GCY-36 act as α-like and β-like sGC subunits and that their function in the URX sensory neurons is sufficient for strong nematode aggregation. Neither GCY-35 nor GCY-36 is absolutely required for C. elegans to aggregate. Instead, these molecules may transduce one of several pathways that induce C. elegans to aggregate or may modulate aggregation by responding to cues in C. elegans body fluid.","lang":"eng"}],"date_created":"2019-03-21T09:42:01Z","citation":{"ama":"Cheung BH., Arellano-Carbajal F, Rybicki I, de Bono M. Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior. <i>Current Biology</i>. 2004;14(12):1105-1111. doi:<a href=\"https://doi.org/10.1016/j.cub.2004.06.027\">10.1016/j.cub.2004.06.027</a>","ista":"Cheung BH., Arellano-Carbajal F, Rybicki I, de Bono M. 2004. Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior. Current Biology. 14(12), 1105–1111.","apa":"Cheung, B. H. ., Arellano-Carbajal, F., Rybicki, I., &#38; de Bono, M. (2004). Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2004.06.027\">https://doi.org/10.1016/j.cub.2004.06.027</a>","chicago":"Cheung, Benny H.H, Fausto Arellano-Carbajal, Irene Rybicki, and Mario de Bono. “Soluble Guanylate Cyclases Act in Neurons Exposed to the Body Fluid to Promote C. Elegans Aggregation Behavior.” <i>Current Biology</i>. Elsevier, 2004. <a href=\"https://doi.org/10.1016/j.cub.2004.06.027\">https://doi.org/10.1016/j.cub.2004.06.027</a>.","ieee":"B. H. . Cheung, F. Arellano-Carbajal, I. Rybicki, and M. de Bono, “Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior,” <i>Current Biology</i>, vol. 14, no. 12. Elsevier, pp. 1105–1111, 2004.","short":"B.H.. Cheung, F. Arellano-Carbajal, I. Rybicki, M. de Bono, Current Biology 14 (2004) 1105–1111.","mla":"Cheung, Benny H. .., et al. “Soluble Guanylate Cyclases Act in Neurons Exposed to the Body Fluid to Promote C. Elegans Aggregation Behavior.” <i>Current Biology</i>, vol. 14, no. 12, Elsevier, 2004, pp. 1105–11, doi:<a href=\"https://doi.org/10.1016/j.cub.2004.06.027\">10.1016/j.cub.2004.06.027</a>."},"extern":"1","author":[{"last_name":"Cheung","first_name":"Benny H.H","full_name":"Cheung, Benny H.H"},{"full_name":"Arellano-Carbajal, Fausto","first_name":"Fausto","last_name":"Arellano-Carbajal"},{"first_name":"Irene","last_name":"Rybicki","full_name":"Rybicki, Irene"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","first_name":"Mario","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario"}],"oa_version":"None","month":"06","type":"journal_article","volume":14,"year":"2004","date_updated":"2021-01-12T08:06:25Z","publisher":"Elsevier","day":"22","publication_status":"published","publication_identifier":{"issn":["0960-9822"]},"external_id":{"pmid":["15203005"]},"quality_controlled":"1","pmid":1,"doi":"10.1016/j.cub.2004.06.027","title":"Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior"},{"page":"1336","issue":"5662","language":[{"iso":"eng"}],"_id":"9454","month":"02","author":[{"first_name":"Simon W.-L.","last_name":"Chan","full_name":"Chan, Simon W.-L."},{"first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"},{"last_name":"Xie","first_name":" Zhixin","full_name":"Xie,  Zhixin"},{"last_name":"Johansen","first_name":" Lisa K.","full_name":"Johansen,  Lisa K."},{"first_name":"James C.","last_name":"Carrington","full_name":"Carrington, James C."},{"full_name":"Jacobsen, Steven E.","first_name":"Steven E.","last_name":"Jacobsen"}],"article_type":"original","citation":{"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.","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>","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>","short":"S.W.-L. Chan, D. Zilberman,  Zhixin Xie,  Lisa K. Johansen, J.C. Carrington, S.E. Jacobsen, Science 303 (2004) 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>.","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."},"keyword":["Multidisciplinary"],"year":"2004","article_processing_charge":"No","title":"RNA silencing genes control de novo DNA methylation","doi":"10.1126/science.1095989","external_id":{"pmid":["14988555"]},"publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"day":"27","date_updated":"2021-12-14T09:13:53Z","date_published":"2004-02-27T00:00:00Z","status":"public","publication":"Science","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":"       303","oa_version":"None","extern":"1","scopus_import":"1","date_created":"2021-06-04T11:12:35Z","volume":303,"type":"journal_article","department":[{"_id":"DaZi"}],"pmid":1,"quality_controlled":"1","publication_status":"published","publisher":"American Association for the Advancement of Science"},{"main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2004.06.055","open_access":"1"}],"type":"journal_article","volume":14,"department":[{"_id":"DaZi"}],"quality_controlled":"1","pmid":1,"publication_status":"published","publisher":"Elsevier","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"}],"publication":"Current Biology","status":"public","date_published":"2004-07-13T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":"        14","oa_version":"Published Version","scopus_import":"1","extern":"1","date_created":"2021-06-07T10:33:00Z","year":"2004","oa":1,"article_processing_charge":"No","doi":"10.1016/j.cub.2004.06.055","title":"Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats","external_id":{"pmid":["15242620 "]},"day":"13","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"date_updated":"2021-12-14T08:52:00Z","page":"1214-1220","issue":"13","language":[{"iso":"eng"}],"_id":"9493","author":[{"first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"},{"last_name":"Cao","first_name":"Xiaofeng","full_name":"Cao, Xiaofeng"},{"last_name":"Johansen","first_name":"Lisa K.","full_name":"Johansen, Lisa K."},{"last_name":"Xie","first_name":"Zhixin","full_name":"Xie, Zhixin"},{"full_name":"Carrington, James C.","first_name":"James C.","last_name":"Carrington"},{"full_name":"Jacobsen, Steven E.","last_name":"Jacobsen","first_name":"Steven E."}],"month":"07","article_type":"original","citation":{"short":"D. Zilberman, X. Cao, L.K. Johansen, Z. Xie, J.C. Carrington, S.E. Jacobsen, Current Biology 14 (2004) 1214–1220.","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.","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>.","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>","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.","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>"}},{"day":"16","publication_identifier":{"eissn":["1465-6906"],"issn":["1474-760X"]},"date_updated":"2021-12-14T08:44:24Z","doi":"10.1186/gb-2004-5-12-249","title":"Silencing of transposons in plant genomes: kick them when they're down","external_id":{"pmid":["15575975"]},"oa":1,"article_processing_charge":"No","year":"2004","article_type":"review","citation":{"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>","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>","ista":"Zilberman D, Henikoff S. 2004. Silencing of transposons in plant genomes: kick them when they’re down. Genome Biology. 5(12), 249.","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.","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>.","short":"D. Zilberman, S. Henikoff, Genome Biology 5 (2004).","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>."},"author":[{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"first_name":"Steven","last_name":"Henikoff","full_name":"Henikoff, Steven"}],"article_number":"249","month":"11","_id":"9511","language":[{"iso":"eng"}],"issue":"12","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"DaZi"}],"quality_controlled":"1","pmid":1,"type":"journal_article","volume":5,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/gb-2004-5-12-249"}],"scopus_import":"1","extern":"1","date_created":"2021-06-07T12:58:06Z","oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":"         5","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":"Genome Biology","status":"public","date_published":"2004-11-16T00:00:00Z"},{"date_updated":"2021-12-14T08:43:57Z","day":"24","publication_identifier":{"issn":["1544-9173"],"eissn":["1545-7885"]},"external_id":{"pmid":["15024409"]},"doi":"10.1371/journal.pbio.0020104","title":"Genetic and functional diversification of small RNA pathways in plants","oa":1,"article_processing_charge":"No","year":"2004","citation":{"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.","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>.","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>.","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>","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>","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."},"article_type":"original","author":[{"first_name":"Zhixin","last_name":"Xie","full_name":"Xie, Zhixin"},{"first_name":"Lisa K.","last_name":"Johansen","full_name":"Johansen, Lisa K."},{"last_name":"Gustafson","first_name":"Adam M.","full_name":"Gustafson, Adam M."},{"full_name":"Kasschau, Kristin D.","first_name":"Kristin D.","last_name":"Kasschau"},{"first_name":"Andrew D. ","last_name":"Lellis","full_name":"Lellis, Andrew D. "},{"first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"},{"full_name":"Jacobsen, Steven E.","first_name":"Steven E.","last_name":"Jacobsen"},{"full_name":"Carrington, James C.","first_name":"James C.","last_name":"Carrington"}],"month":"02","_id":"9517","language":[{"iso":"eng"}],"issue":"5","page":"0642-0652","publisher":"Public Library of Science","publication_status":"published","quality_controlled":"1","pmid":1,"department":[{"_id":"DaZi"}],"type":"journal_article","volume":2,"main_file_link":[{"url":"https://doi.org/10.1371/journal.pbio.0020104","open_access":"1"}],"date_created":"2021-06-07T14:12:08Z","extern":"1","scopus_import":"1","oa_version":"Published Version","intvolume":"         2","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication":"PLoS Biology","status":"public","date_published":"2004-02-24T00:00:00Z","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."}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"         1","abstract":[{"text":"In this paper, we describe six algorithmic problems that arise in web search engines and that are not or only partially solved: (1) Uniformly sampling of web pages; (2) modeling the web graph; (3) finding duplicate hosts; (4) finding top gainers and losers in data streams; (5) finding large dense bipartite graphs; and (6) understanding how eigenvectors partition the web.","lang":"eng"}],"publication":"Internet Mathematics","status":"public","date_published":"2004-01-01T00:00:00Z","extern":"1","scopus_import":"1","date_created":"2022-08-08T11:55:53Z","oa_version":"Published Version","type":"journal_article","volume":1,"main_file_link":[{"url":"https://doi.org/10.1080/15427951.2004.10129079","open_access":"1"}],"publication_status":"published","publisher":"Internet Mathematics","quality_controlled":"1","language":[{"iso":"eng"}],"_id":"11762","page":"115-123","issue":"1","article_type":"original","citation":{"ieee":"M. H. Henzinger, “Algorithmic challenges in web search engines,” <i>Internet Mathematics</i>, vol. 1, no. 1. Internet Mathematics, pp. 115–123, 2004.","chicago":"Henzinger, Monika H. “Algorithmic Challenges in Web Search Engines.” <i>Internet Mathematics</i>. Internet Mathematics, 2004. <a href=\"https://doi.org/10.1080/15427951.2004.10129079\">https://doi.org/10.1080/15427951.2004.10129079</a>.","short":"M.H. Henzinger, Internet Mathematics 1 (2004) 115–123.","mla":"Henzinger, Monika H. “Algorithmic Challenges in Web Search Engines.” <i>Internet Mathematics</i>, vol. 1, no. 1, Internet Mathematics, 2004, pp. 115–23, doi:<a href=\"https://doi.org/10.1080/15427951.2004.10129079\">10.1080/15427951.2004.10129079</a>.","ama":"Henzinger MH. Algorithmic challenges in web search engines. <i>Internet Mathematics</i>. 2004;1(1):115-123. doi:<a href=\"https://doi.org/10.1080/15427951.2004.10129079\">10.1080/15427951.2004.10129079</a>","apa":"Henzinger, M. H. (2004). Algorithmic challenges in web search engines. <i>Internet Mathematics</i>. Internet Mathematics. <a href=\"https://doi.org/10.1080/15427951.2004.10129079\">https://doi.org/10.1080/15427951.2004.10129079</a>","ista":"Henzinger MH. 2004. Algorithmic challenges in web search engines. Internet Mathematics. 1(1), 115–123."},"author":[{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H"}],"month":"01","oa":1,"article_processing_charge":"No","year":"2004","day":"01","publication_identifier":{"eissn":["1944-9488"],"issn":["1542-7951"]},"date_updated":"2023-02-10T07:47:21Z","doi":"10.1080/15427951.2004.10129079","title":"Algorithmic challenges in web search engines"},{"abstract":[{"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.","lang":"eng"}],"page":"3","date_published":"2004-07-01T00:00:00Z","status":"public","publication":"31st International Colloquium on Automata, Languages and Programming","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11800","language":[{"iso":"eng"}],"intvolume":"      3142","month":"07","author":[{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"}],"oa_version":"None","alternative_title":["LNCS"],"extern":"1","scopus_import":"1","date_created":"2022-08-11T12:38:58Z","citation":{"short":"M.H. Henzinger, in:, 31st International Colloquium on Automata, Languages and Programming, Springer Nature, 2004, p. 3.","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>.","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.","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>","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.","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>"},"conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","location":"Turku, Finland","end_date":"2004-07-16","start_date":"2004-07-12"},"year":"2004","volume":3142,"type":"conference","article_processing_charge":"No","title":"The past, present, and future of web search engines","doi":"10.1007/978-3-540-27836-8_2","quality_controlled":"1","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"]},"publication_status":"published","day":"01","publisher":"Springer Nature","date_updated":"2023-02-13T11:45:25Z"},{"language":[{"iso":"eng"}],"_id":"11801","intvolume":"      3221","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"2th Annual European Symposium on Algorithms","date_published":"2004-09-01T00:00:00Z","status":"public","page":"3","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."}],"date_created":"2022-08-11T13:18:05Z","citation":{"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>.","short":"M.H. Henzinger, in:, 2th Annual European Symposium on Algorithms, Springer Nature, 2004, p. 3.","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.","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>.","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>","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.","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>"},"scopus_import":"1","extern":"1","alternative_title":["LNCS"],"oa_version":"None","author":[{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H"}],"month":"09","article_processing_charge":"No","type":"conference","volume":3221,"year":"2004","conference":{"location":"Bergen, Norway","name":"ESA: European Symposium on Algorithms","start_date":"2004-09-14","end_date":"2004-09-17"},"date_updated":"2023-02-13T11:47:26Z","publisher":"Springer Nature","day":"01","publication_status":"published","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":[" 3540230254"]},"quality_controlled":"1","doi":"10.1007/978-3-540-30140-0_2","title":"Algorithmic aspects of web search engines"},{"year":"2004","conference":{"name":"Document Recognition and Retrieval XI","location":"San Jose, CA, United States","end_date":"2004-01-22","start_date":"2004-01-21"},"article_processing_charge":"No","volume":5296,"type":"conference","quality_controlled":"1","title":"The past, present, and future of web information retrieval","doi":"10.1117/12.537534","publisher":"Society of Photo-Optical Instrumentation Engineers","date_updated":"2023-02-17T10:05:19Z","publication_status":"published","publication_identifier":{"issn":["0277-786X"]},"day":"01","date_published":"2004-01-01T00:00:00Z","status":"public","publication":"SPIE Proceedings","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."}],"page":"23 - 26","_id":"11859","language":[{"iso":"eng"}],"intvolume":"      5296","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","oa_version":"None","author":[{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"}],"date_created":"2022-08-16T08:46:41Z","citation":{"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.","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>.","short":"M.H. Henzinger, in:, SPIE Proceedings, Society of Photo-Optical Instrumentation Engineers, 2004, pp. 23–26.","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>.","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>","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>","ista":"Henzinger MH. 2004. The past, present, and future of web information retrieval. SPIE Proceedings. Document Recognition and Retrieval XI vol. 5296, 23–26."},"scopus_import":"1","extern":"1"},{"month":"04","author":[{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"last_name":"Lawrence","first_name":"Steve","full_name":"Lawrence, Steve"}],"citation":{"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.","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>.","short":"M.H. Henzinger, S. Lawrence, Proceedings of the National Academy of Sciences 101 (2004) 5186–5191.","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>.","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>","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>","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."},"article_type":"original","issue":"suppl_1","page":"5186-5191","_id":"11877","language":[{"iso":"eng"}],"external_id":{"pmid":["14745041"]},"title":"Extracting knowledge from the World Wide Web","doi":"10.1073/pnas.0307528100","date_updated":"2023-02-17T12:21:43Z","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"day":"06","year":"2004","oa":1,"article_processing_charge":"No","oa_version":"Published Version","date_created":"2022-08-16T13:06:10Z","scopus_import":"1","extern":"1","date_published":"2004-04-06T00:00:00Z","status":"public","publication":"Proceedings of the National Academy of Sciences","abstract":[{"lang":"eng","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."}],"intvolume":"       101","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"quality_controlled":"1","publisher":"Proceedings of the National Academy of Sciences","publication_status":"published","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC387294/","open_access":"1"}],"volume":101,"type":"journal_article"},{"publisher":"Unknown","date_updated":"2021-01-12T06:55:14Z","publication_status":"published","day":"17","quality_controlled":0,"title":"Equal sums of three powers","doi":"10.1007/s00222-004-0360-9","volume":157,"type":"journal_article","year":"2004","date_created":"2018-12-11T11:45:13Z","citation":{"apa":"Browning, T. D., &#38; Heath Brown, R. (2004). Equal sums of three powers. <i>Inventiones Mathematicae</i>. Unknown. <a href=\"https://doi.org/10.1007/s00222-004-0360-9\">https://doi.org/10.1007/s00222-004-0360-9</a>","ista":"Browning TD, Heath Brown R. 2004. Equal sums of three powers. Inventiones Mathematicae. 157(3), 553–573.","ama":"Browning TD, Heath Brown R. Equal sums of three powers. <i>Inventiones Mathematicae</i>. 2004;157(3):553-573. doi:<a href=\"https://doi.org/10.1007/s00222-004-0360-9\">10.1007/s00222-004-0360-9</a>","mla":"Browning, Timothy D., and Roger Heath Brown. “Equal Sums of Three Powers.” <i>Inventiones Mathematicae</i>, vol. 157, no. 3, Unknown, 2004, pp. 553–73, doi:<a href=\"https://doi.org/10.1007/s00222-004-0360-9\">10.1007/s00222-004-0360-9</a>.","short":"T.D. Browning, R. Heath Brown, Inventiones Mathematicae 157 (2004) 553–573.","ieee":"T. D. Browning and R. Heath Brown, “Equal sums of three powers,” <i>Inventiones Mathematicae</i>, vol. 157, no. 3. Unknown, pp. 553–573, 2004.","chicago":"Browning, Timothy D, and Roger Heath Brown. “Equal Sums of Three Powers.” <i>Inventiones Mathematicae</i>. Unknown, 2004. <a href=\"https://doi.org/10.1007/s00222-004-0360-9\">https://doi.org/10.1007/s00222-004-0360-9</a>."},"extern":1,"month":"03","author":[{"last_name":"Browning","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","full_name":"Timothy Browning"},{"first_name":"Roger","last_name":"Heath Brown","full_name":"Heath-Brown, Roger"}],"intvolume":"       157","_id":"209","status":"public","date_published":"2004-03-17T00:00:00Z","publication":"Inventiones Mathematicae","publist_id":"7703","issue":"3","page":"553 - 573"}]