---
_id: '902'
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.'
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.
  The 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.
author:
- first_name: Cristian
  full_name: Castillo-Davis, Cristian I
  last_name: Castillo Davis
- first_name: Fyodor
  full_name: Fyodor Kondrashov
  id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
  last_name: Kondrashov
  orcid: 0000-0001-8243-4694
- first_name: Daniel
  full_name: Hartl, Daniel L
  last_name: Hartl
- first_name: Rob
  full_name: Kulathinal, Rob J
  last_name: Kulathinal
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>'
  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.'
  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.'
  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.
date_created: 2018-12-11T11:49:06Z
date_published: 2004-05-01T00:00:00Z
date_updated: 2021-01-12T08:21:47Z
day: '01'
doi: 10.1101/gr.2195604
extern: 1
intvolume: '        14'
issue: '5'
month: '05'
page: 802 - 811
publication: Genome Research
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '6750'
quality_controlled: 0
status: public
title: 'The functional genomic distribution of protein divergence in two animal phyla:
  Coevolution, genomic conflict, and constraint'
type: journal_article
volume: 14
year: '2004'
...
---
_id: '7333'
abstract:
- lang: eng
  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.
article_processing_charge: No
article_type: original
author:
- first_name: M.
  full_name: Santis, M.
  last_name: Santis
- first_name: D.
  full_name: Schmid, D.
  last_name: Schmid
- first_name: M.
  full_name: Ruge, M.
  last_name: Ruge
- first_name: Stefan Alexander
  full_name: Freunberger, Stefan Alexander
  id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
  last_name: Freunberger
  orcid: 0000-0003-2902-5319
- first_name: F.N.
  full_name: Büchi, F.N.
  last_name: Büchi
citation:
  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>
  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>
  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.
  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.
date_created: 2020-01-15T12:24:14Z
date_published: 2004-08-01T00:00:00Z
date_updated: 2021-01-12T08:13:08Z
day: '01'
doi: 10.1002/fuce.200400028
extern: '1'
intvolume: '         4'
issue: '3'
language:
- iso: eng
month: '08'
oa_version: None
page: 214-218
publication: Fuel Cells
publication_identifier:
  issn:
  - 1615-6846
  - 1615-6854
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Modular stack-internal air humidification concept-verification in a 1 kW stack
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2004'
...
---
_id: '7334'
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. '
article_processing_charge: No
article_type: original
author:
- first_name: John
  full_name: Mantzaras, John
  last_name: Mantzaras
- first_name: Stefan Alexander
  full_name: Freunberger, Stefan Alexander
  id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
  last_name: Freunberger
  orcid: 0000-0003-2902-5319
- first_name: Felix N.
  full_name: Büchi, Felix N.
  last_name: Büchi
- first_name: Markus
  full_name: Roos, Markus
  last_name: Roos
- first_name: Wilhelm
  full_name: Brandstätter, Wilhelm
  last_name: Brandstätter
- first_name: Michel
  full_name: Prestat, Michel
  last_name: Prestat
- first_name: Ludwig J.
  full_name: Gauckler, Ludwig J.
  last_name: Gauckler
- first_name: Bernhard
  full_name: Andreaus, Bernhard
  last_name: Andreaus
- first_name: Faegheh
  full_name: Hajbolouri, Faegheh
  last_name: Hajbolouri
- first_name: Stephan M.
  full_name: Senn, Stephan M.
  last_name: Senn
- first_name: Dimos
  full_name: Poulikakos, Dimos
  last_name: Poulikakos
- first_name: Andreas K.
  full_name: Chaniotis, Andreas K.
  last_name: Chaniotis
- first_name: Diego
  full_name: Larrain, Diego
  last_name: Larrain
- first_name: Nordahl
  full_name: Autissier, Nordahl
  last_name: Autissier
- first_name: François
  full_name: Maréchal, François
  last_name: Maréchal
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>
  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>.
  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.
  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.
  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
date_published: 2004-12-01T00:00:00Z
date_updated: 2021-01-12T08:13:09Z
day: '01'
doi: 10.2533/000942904777677029
extern: '1'
intvolume: '        58'
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
page: 857-868
publication: CHIMIA International Journal for Chemistry
publication_identifier:
  issn:
  - 0009-4293
publication_status: published
publisher: Swiss Chemical Society
quality_controlled: '1'
status: public
title: Fuel cell modeling and simulations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 58
year: '2004'
...
---
_id: '7706'
abstract:
- lang: eng
  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.'
article_processing_charge: No
article_type: original
author:
- first_name: Anne
  full_name: Brunet, Anne
  last_name: Brunet
- first_name: Lora Beatrice Jaeger
  full_name: Sweeney, Lora Beatrice Jaeger
  id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
  last_name: Sweeney
  orcid: 0000-0001-9242-5601
- first_name: 'J Fitzhugh '
  full_name: 'Sturgill, J Fitzhugh '
  last_name: Sturgill
- first_name: Katrin
  full_name: Chua, Katrin
  last_name: Chua
- first_name: Paul
  full_name: Greer, Paul
  last_name: Greer
- first_name: Yingxi
  full_name: Lin, Yingxi
  last_name: Lin
- first_name: Hien
  full_name: Tran, Hien
  last_name: Tran
- first_name: Sarah
  full_name: Ross, Sarah
  last_name: Ross
- first_name: Raul
  full_name: Mostoslavsky, Raul
  last_name: Mostoslavsky
- first_name: Haim
  full_name: Cohen, Haim
  last_name: Cohen
- first_name: Linda
  full_name: Hu, Linda
  last_name: Hu
- first_name: Hwei-Ling
  full_name: Chen, Hwei-Ling
  last_name: Chen
- first_name: Mark
  full_name: Jedrychowski, Mark
  last_name: Jedrychowski
- first_name: Steven
  full_name: Gygi, Steven
  last_name: Gygi
- first_name: David
  full_name: Sinclair, David
  last_name: Sinclair
- first_name: Frederick
  full_name: Alt, Frederick
  last_name: Alt
- first_name: Michael
  full_name: Greenberg, Michael
  last_name: Greenberg
citation:
  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>
  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>
  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.
  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.
  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>.
  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.
date_created: 2020-04-30T10:37:41Z
date_published: 2004-03-26T00:00:00Z
date_updated: 2024-01-31T10:14:17Z
day: '26'
doi: 10.1126/science.1094637
extern: '1'
intvolume: '       303'
issue: '5666'
language:
- iso: eng
month: '03'
oa_version: None
page: 2011-2015
publication: Science
publication_identifier:
  issn:
  - 0036-8075
  - 1095-9203
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
status: public
title: Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 303
year: '2004'
...
---
_id: '1963'
abstract:
- lang: eng
  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.
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.)
author:
- first_name: Aygun
  full_name: Mamedova, Aygun A
  last_name: Mamedova
- first_name: Peter
  full_name: Holt, Peter J
  last_name: Holt
- first_name: Joe
  full_name: Carroll, Joe D
  last_name: Carroll
- first_name: Leonid A
  full_name: Leonid Sazanov
  id: 338D39FE-F248-11E8-B48F-1D18A9856A87
  last_name: Sazanov
  orcid: 0000-0002-0977-7989
citation:
  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>
  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>
  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.
  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.
date_created: 2018-12-11T11:54:56Z
date_published: 2004-05-28T00:00:00Z
date_updated: 2021-01-12T06:54:22Z
day: '28'
doi: 10.1074/jbc.M401539200
extern: 1
intvolume: '       279'
issue: '22'
month: '05'
page: 23830 - 23836
publication: Journal of Biological Chemistry
publication_status: published
publisher: American Society for Biochemistry and Molecular Biology
publist_id: '5123'
quality_controlled: 0
status: public
title: Substrate-induced conformational change in bacterial complex I
type: journal_article
volume: 279
year: '2004'
...
---
_id: '13434'
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.
article_processing_charge: No
article_type: original
author:
- first_name: C. J.
  full_name: Campbell, C. J.
  last_name: Campbell
- first_name: M.
  full_name: Fialkowski, M.
  last_name: Fialkowski
- first_name: Rafal
  full_name: Klajn, Rafal
  id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
  last_name: Klajn
- first_name: I. T.
  full_name: Bensemann, I. T.
  last_name: Bensemann
- first_name: B. A.
  full_name: Grzybowski, B. A.
  last_name: Grzybowski
citation:
  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>
  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.
  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.
  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>.
  short: C.J. Campbell, M. Fialkowski, R. Klajn, I.T. Bensemann, B.A. Grzybowski,
    Advanced Materials 16 (2004) 1912–1917.
date_created: 2023-08-01T10:39:09Z
date_published: 2004-11-14T00:00:00Z
date_updated: 2023-08-08T12:41:23Z
day: '14'
doi: 10.1002/adma.200400383
extern: '1'
intvolume: '        16'
issue: '21'
keyword:
- Mechanical Engineering
- Mechanics of Materials
- General Materials Science
language:
- iso: eng
month: '11'
oa_version: None
page: 1912-1917
publication: Advanced Materials
publication_identifier:
  eissn:
  - 1521-4095
  issn:
  - 0935-9648
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Color micro- and nanopatterning with counter-propagating reaction-diffusion
  fronts
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2004'
...
---
_id: '13435'
abstract:
- lang: eng
  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.
article_processing_charge: No
article_type: original
author:
- first_name: Rafal
  full_name: Klajn, Rafal
  id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
  last_name: Klajn
- first_name: Marcin
  full_name: Fialkowski, Marcin
  last_name: Fialkowski
- first_name: Igor T.
  full_name: Bensemann, Igor T.
  last_name: Bensemann
- first_name: Agnieszka
  full_name: Bitner, Agnieszka
  last_name: Bitner
- first_name: C. J.
  full_name: Campbell, C. J.
  last_name: Campbell
- first_name: Kyle
  full_name: Bishop, Kyle
  last_name: Bishop
- first_name: Stoyan
  full_name: Smoukov, Stoyan
  last_name: Smoukov
- first_name: Bartosz A.
  full_name: Grzybowski, Bartosz A.
  last_name: Grzybowski
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>
  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.
  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.
  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>.
  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.
date_created: 2023-08-01T10:39:23Z
date_published: 2004-09-19T00:00:00Z
date_updated: 2023-08-08T12:42:51Z
day: '19'
doi: 10.1038/nmat1231
extern: '1'
external_id:
  pmid:
  - '15378052'
intvolume: '         3'
keyword:
- Mechanical Engineering
- Mechanics of Materials
- Condensed Matter Physics
- General Materials Science
- General Chemistry
language:
- iso: eng
month: '09'
oa_version: None
page: 729-735
pmid: 1
publication: Nature Materials
publication_identifier:
  eissn:
  - 1476-4660
  issn:
  - 1476-1122
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Multicolour micropatterning of thin films of dry gels
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2004'
...
---
_id: '1456'
abstract:
- lang: eng
  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.
acknowledgement: |-
  Hausel’s work supported by a Miller Research Fellowship at the University of California, Berkeley.
  Hunsicker’s work partially supported by Stanford University.
  Mazzeo’s work supported by National Science Foundation grant numbers DMS-991975 and DMS-0204730 and
  by the Mathematical Sciences Research Institute.
author:
- first_name: Tamas
  full_name: Tamas Hausel
  id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
  last_name: Hausel
- first_name: Eugénie
  full_name: Hunsicker, Eugénie
  last_name: Hunsicker
- first_name: Rafe
  full_name: Mazzeo, Rafe R
  last_name: Mazzeo
citation:
  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>
  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>
  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>.
  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.
  ista: Hausel T, Hunsicker E, Mazzeo R. 2004. Hodge cohomology of gravitational instantons.
    Duke Mathematical Journal. 122(3), 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>.
  short: T. Hausel, E. Hunsicker, R. Mazzeo, Duke Mathematical Journal 122 (2004)
    485–548.
date_created: 2018-12-11T11:52:08Z
date_published: 2004-04-15T00:00:00Z
date_updated: 2021-01-12T06:50:52Z
day: '15'
doi: 10.1215/S0012-7094-04-12233-X
extern: 1
intvolume: '       122'
issue: '3'
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/math/0207169
month: '04'
oa: 1
page: 485 - 548
publication: Duke Mathematical Journal
publication_status: published
publisher: Duke University Press
publist_id: '5737'
quality_controlled: 0
status: public
title: Hodge cohomology of gravitational instantons
type: journal_article
volume: 122
year: '2004'
...
---
_id: '1464'
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). "
author:
- first_name: Tamas
  full_name: Tamas Hausel
  id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
  last_name: Hausel
- first_name: Michael
  full_name: Thaddeus, Michael
  last_name: Thaddeus
citation:
  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>
  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>.
  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.
  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.
  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.
date_created: 2018-12-11T11:52:10Z
date_published: 2004-05-01T00:00:00Z
date_updated: 2021-01-12T06:50:55Z
day: '01'
doi: 10.1112/S0024611503014618
extern: 1
intvolume: '        88'
issue: '3'
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/math/0003093
month: '05'
oa: 1
page: 632 - 658
publication: Proceedings of the London Mathematical Society
publication_status: published
publisher: Oxford University Press
publist_id: '5736'
quality_controlled: 0
status: public
title: Generators for the cohomology ring of the moduli space of rank 2 higgs bundles
type: journal_article
volume: 88
year: '2004'
...
---
_id: '6155'
abstract:
- lang: eng
  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.'
author:
- first_name: Benny H.H
  full_name: Cheung, Benny H.H
  last_name: Cheung
- first_name: Fausto
  full_name: Arellano-Carbajal, Fausto
  last_name: Arellano-Carbajal
- first_name: Irene
  full_name: Rybicki, Irene
  last_name: Rybicki
- first_name: Mario
  full_name: de Bono, Mario
  id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
  last_name: de Bono
  orcid: 0000-0001-8347-0443
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>
  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.
  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.
  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>.
  short: B.H.. Cheung, F. Arellano-Carbajal, I. Rybicki, M. de Bono, Current Biology
    14 (2004) 1105–1111.
date_created: 2019-03-21T09:42:01Z
date_published: 2004-06-22T00:00:00Z
date_updated: 2021-01-12T08:06:25Z
day: '22'
doi: 10.1016/j.cub.2004.06.027
extern: '1'
external_id:
  pmid:
  - '15203005'
intvolume: '        14'
issue: '12'
language:
- iso: eng
month: '06'
oa_version: None
page: 1105-1111
pmid: 1
publication: Current Biology
publication_identifier:
  issn:
  - 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Soluble guanylate cyclases act in neurons exposed to the body fluid to promote
  C. elegans aggregation behavior
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2004'
...
---
_id: '9454'
article_processing_charge: No
article_type: original
author:
- first_name: Simon W.-L.
  full_name: Chan, Simon W.-L.
  last_name: Chan
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
- first_name: ' Zhixin'
  full_name: Xie,  Zhixin
  last_name: Xie
- first_name: ' Lisa K.'
  full_name: Johansen,  Lisa K.
  last_name: Johansen
- first_name: James C.
  full_name: Carrington, James C.
  last_name: Carrington
- first_name: Steven E.
  full_name: Jacobsen, Steven E.
  last_name: Jacobsen
citation:
  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>
  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>
  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.
  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>.
  short: S.W.-L. Chan, D. Zilberman,  Zhixin Xie,  Lisa K. Johansen, J.C. Carrington,
    S.E. Jacobsen, Science 303 (2004) 1336.
date_created: 2021-06-04T11:12:35Z
date_published: 2004-02-27T00:00:00Z
date_updated: 2021-12-14T09:13:53Z
day: '27'
department:
- _id: DaZi
doi: 10.1126/science.1095989
extern: '1'
external_id:
  pmid:
  - '14988555'
intvolume: '       303'
issue: '5662'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '02'
oa_version: None
page: '1336'
pmid: 1
publication: Science
publication_identifier:
  eissn:
  - 1095-9203
  issn:
  - 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: RNA silencing genes control de novo DNA methylation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 303
year: '2004'
...
---
_id: '9493'
abstract:
- lang: eng
  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.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
- first_name: Xiaofeng
  full_name: Cao, Xiaofeng
  last_name: Cao
- first_name: Lisa K.
  full_name: Johansen, Lisa K.
  last_name: Johansen
- first_name: Zhixin
  full_name: Xie, Zhixin
  last_name: Xie
- first_name: James C.
  full_name: Carrington, James C.
  last_name: Carrington
- first_name: Steven E.
  full_name: Jacobsen, Steven E.
  last_name: Jacobsen
citation:
  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>
  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>
  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>.
  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.
  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.
  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>.
  short: D. Zilberman, X. Cao, L.K. Johansen, Z. Xie, J.C. Carrington, S.E. Jacobsen,
    Current Biology 14 (2004) 1214–1220.
date_created: 2021-06-07T10:33:00Z
date_published: 2004-07-13T00:00:00Z
date_updated: 2021-12-14T08:52:00Z
day: '13'
department:
- _id: DaZi
doi: 10.1016/j.cub.2004.06.055
extern: '1'
external_id:
  pmid:
  - '15242620 '
intvolume: '        14'
issue: '13'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1016/j.cub.2004.06.055
month: '07'
oa: 1
oa_version: Published Version
page: 1214-1220
pmid: 1
publication: Current Biology
publication_identifier:
  eissn:
  - 1879-0445
  issn:
  - 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by
  inverted repeats
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 14
year: '2004'
...
---
_id: '9511'
abstract:
- lang: eng
  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.
article_number: '249'
article_processing_charge: No
article_type: review
author:
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
- first_name: Steven
  full_name: Henikoff, Steven
  last_name: Henikoff
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>'
  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>.'
  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.'
  ista: 'Zilberman D, Henikoff S. 2004. Silencing of transposons in plant genomes:
    kick them when they’re down. Genome Biology. 5(12), 249.'
  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>.'
  short: D. Zilberman, S. Henikoff, Genome Biology 5 (2004).
date_created: 2021-06-07T12:58:06Z
date_published: 2004-11-16T00:00:00Z
date_updated: 2021-12-14T08:44:24Z
day: '16'
department:
- _id: DaZi
doi: 10.1186/gb-2004-5-12-249
extern: '1'
external_id:
  pmid:
  - '15575975'
intvolume: '         5'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1186/gb-2004-5-12-249
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
  eissn:
  - 1465-6906
  issn:
  - 1474-760X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Silencing of transposons in plant genomes: kick them when they''re down'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 5
year: '2004'
...
---
_id: '9517'
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.
article_processing_charge: No
article_type: original
author:
- first_name: Zhixin
  full_name: Xie, Zhixin
  last_name: Xie
- first_name: Lisa K.
  full_name: Johansen, Lisa K.
  last_name: Johansen
- first_name: Adam M.
  full_name: Gustafson, Adam M.
  last_name: Gustafson
- first_name: Kristin D.
  full_name: Kasschau, Kristin D.
  last_name: Kasschau
- first_name: 'Andrew D. '
  full_name: 'Lellis, Andrew D. '
  last_name: Lellis
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
- first_name: Steven E.
  full_name: Jacobsen, Steven E.
  last_name: Jacobsen
- first_name: James C.
  full_name: Carrington, James C.
  last_name: Carrington
citation:
  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>
  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>.
  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.
  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>.
  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.
date_created: 2021-06-07T14:12:08Z
date_published: 2004-02-24T00:00:00Z
date_updated: 2021-12-14T08:43:57Z
day: '24'
department:
- _id: DaZi
doi: 10.1371/journal.pbio.0020104
extern: '1'
external_id:
  pmid:
  - '15024409'
intvolume: '         2'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1371/journal.pbio.0020104
month: '02'
oa: 1
oa_version: Published Version
page: 0642-0652
pmid: 1
publication: PLoS Biology
publication_identifier:
  eissn:
  - 1545-7885
  issn:
  - 1544-9173
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic and functional diversification of small RNA pathways in plants
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 2
year: '2004'
...
---
_id: '11762'
abstract:
- lang: eng
  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.'
article_processing_charge: No
article_type: original
author:
- first_name: Monika H
  full_name: Henzinger, Monika H
  id: 540c9bbd-f2de-11ec-812d-d04a5be85630
  last_name: Henzinger
  orcid: 0000-0002-5008-6530
citation:
  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>
  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>.
  ieee: M. H. Henzinger, “Algorithmic challenges in web search engines,” <i>Internet
    Mathematics</i>, vol. 1, no. 1. Internet Mathematics, pp. 115–123, 2004.
  ista: Henzinger MH. 2004. Algorithmic challenges in web search engines. Internet
    Mathematics. 1(1), 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>.
  short: M.H. Henzinger, Internet Mathematics 1 (2004) 115–123.
date_created: 2022-08-08T11:55:53Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2023-02-10T07:47:21Z
day: '01'
doi: 10.1080/15427951.2004.10129079
extern: '1'
intvolume: '         1'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1080/15427951.2004.10129079
month: '01'
oa: 1
oa_version: Published Version
page: 115-123
publication: Internet Mathematics
publication_identifier:
  eissn:
  - 1944-9488
  issn:
  - 1542-7951
publication_status: published
publisher: Internet Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Algorithmic challenges in web search engines
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2004'
...
---
_id: '11800'
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."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Monika H
  full_name: Henzinger, Monika H
  id: 540c9bbd-f2de-11ec-812d-d04a5be85630
  last_name: Henzinger
  orcid: 0000-0002-5008-6530
citation:
  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>'
  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>'
  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>.
  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.
  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.'
  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>.
  short: M.H. Henzinger, in:, 31st International Colloquium on Automata, Languages
    and Programming, Springer Nature, 2004, p. 3.
conference:
  end_date: 2004-07-16
  location: Turku, Finland
  name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
  start_date: 2004-07-12
date_created: 2022-08-11T12:38:58Z
date_published: 2004-07-01T00:00:00Z
date_updated: 2023-02-13T11:45:25Z
day: '01'
doi: 10.1007/978-3-540-27836-8_2
extern: '1'
intvolume: '      3142'
language:
- iso: eng
month: '07'
oa_version: None
page: '3'
publication: 31st International Colloquium on Automata, Languages and Programming
publication_identifier:
  eissn:
  - 1611-3349
  issn:
  - 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The past, present, and future of web search engines
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3142
year: '2004'
...
---
_id: '11801'
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."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Monika H
  full_name: Henzinger, Monika H
  id: 540c9bbd-f2de-11ec-812d-d04a5be85630
  last_name: Henzinger
  orcid: 0000-0002-5008-6530
citation:
  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>'
  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>'
  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.
  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>.
  short: M.H. Henzinger, in:, 2th Annual European Symposium on Algorithms, Springer
    Nature, 2004, p. 3.
conference:
  end_date: 2004-09-17
  location: Bergen, Norway
  name: 'ESA: European Symposium on Algorithms'
  start_date: 2004-09-14
date_created: 2022-08-11T13:18:05Z
date_published: 2004-09-01T00:00:00Z
date_updated: 2023-02-13T11:47:26Z
day: '01'
doi: 10.1007/978-3-540-30140-0_2
extern: '1'
intvolume: '      3221'
language:
- iso: eng
month: '09'
oa_version: None
page: '3'
publication: 2th Annual European Symposium on Algorithms
publication_identifier:
  eissn:
  - 1611-3349
  isbn:
  - ' 3540230254'
  issn:
  - 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Algorithmic aspects of web search engines
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3221
year: '2004'
...
---
_id: '11859'
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.
article_processing_charge: No
author:
- first_name: Monika H
  full_name: Henzinger, Monika H
  id: 540c9bbd-f2de-11ec-812d-d04a5be85630
  last_name: Henzinger
  orcid: 0000-0002-5008-6530
citation:
  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>'
  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>.
  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.
  ista: Henzinger MH. 2004. The past, present, and future of web information retrieval.
    SPIE Proceedings. Document Recognition and Retrieval XI vol. 5296, 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>.
  short: M.H. Henzinger, in:, SPIE Proceedings, Society of Photo-Optical Instrumentation
    Engineers, 2004, pp. 23–26.
conference:
  end_date: 2004-01-22
  location: San Jose, CA, United States
  name: Document Recognition and Retrieval XI
  start_date: 2004-01-21
date_created: 2022-08-16T08:46:41Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2023-02-17T10:05:19Z
day: '01'
doi: 10.1117/12.537534
extern: '1'
intvolume: '      5296'
language:
- iso: eng
month: '01'
oa_version: None
page: 23 - 26
publication: SPIE Proceedings
publication_identifier:
  issn:
  - 0277-786X
publication_status: published
publisher: Society of Photo-Optical Instrumentation Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: The past, present, and future of web information retrieval
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5296
year: '2004'
...
---
_id: '11877'
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.
article_processing_charge: No
article_type: original
author:
- first_name: Monika H
  full_name: Henzinger, Monika H
  id: 540c9bbd-f2de-11ec-812d-d04a5be85630
  last_name: Henzinger
  orcid: 0000-0002-5008-6530
- first_name: Steve
  full_name: Lawrence, Steve
  last_name: Lawrence
citation:
  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>
  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>.
  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.
  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.
  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>.
  short: M.H. Henzinger, S. Lawrence, Proceedings of the National Academy of Sciences
    101 (2004) 5186–5191.
date_created: 2022-08-16T13:06:10Z
date_published: 2004-04-06T00:00:00Z
date_updated: 2023-02-17T12:21:43Z
day: '06'
doi: 10.1073/pnas.0307528100
extern: '1'
external_id:
  pmid:
  - '14745041'
intvolume: '       101'
issue: suppl_1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC387294/
month: '04'
oa: 1
oa_version: Published Version
page: 5186-5191
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
  eissn:
  - 1091-6490
  issn:
  - 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extracting knowledge from the World Wide Web
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 101
year: '2004'
...
---
_id: '209'
author:
- first_name: Timothy D
  full_name: Timothy Browning
  id: 35827D50-F248-11E8-B48F-1D18A9856A87
  last_name: Browning
  orcid: 0000-0002-8314-0177
- first_name: Roger
  full_name: Heath-Brown, Roger
  last_name: Heath Brown
citation:
  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>
  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>
  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>.
  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.
  ista: Browning TD, Heath Brown R. 2004. Equal sums of three powers. Inventiones
    Mathematicae. 157(3), 553–573.
  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.
date_created: 2018-12-11T11:45:13Z
date_published: 2004-03-17T00:00:00Z
date_updated: 2021-01-12T06:55:14Z
day: '17'
doi: 10.1007/s00222-004-0360-9
extern: 1
intvolume: '       157'
issue: '3'
month: '03'
page: 553 - 573
publication: Inventiones Mathematicae
publication_status: published
publisher: Unknown
publist_id: '7703'
quality_controlled: 0
status: public
title: Equal sums of three powers
type: journal_article
volume: 157
year: '2004'
...
