Search Results - (Author, Cooperation:S. Brunak)

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  1. 1
    M. E. Allentoft ; M. Sikora ; K. G. Sjogren ; S. Rasmussen ; M. Rasmussen ; J. Stenderup ; P. B. Damgaard ; H. Schroeder ; T. Ahlstrom ; L. Vinner ; A. S. Malaspinas ; A. Margaryan ; T. Higham ; D. Chivall ; N. Lynnerup ; L. Harvig ; J. Baron ; P. Della Casa ; P. Dabrowski ; P. R. Duffy ; A. V. Ebel ; A. Epimakhov ; K. Frei ; M. Furmanek ; T. Gralak ; A. Gromov ; S. Gronkiewicz ; G. Grupe ; T. Hajdu ; R. Jarysz ; V. Khartanovich ; A. Khokhlov ; V. Kiss ; J. Kolar ; A. Kriiska ; I. Lasak ; C. Longhi ; G. McGlynn ; A. Merkevicius ; I. Merkyte ; M. Metspalu ; R. Mkrtchyan ; V. Moiseyev ; L. Paja ; G. Palfi ; D. Pokutta ; L. Pospieszny ; T. D. Price ; L. Saag ; M. Sablin ; N. Shishlina ; V. Smrcka ; V. I. Soenov ; V. Szeverenyi ; G. Toth ; S. V. Trifanova ; L. Varul ; M. Vicze ; L. Yepiskoposyan ; V. Zhitenev ; L. Orlando ; T. Sicheritz-Ponten ; S. Brunak ; R. Nielsen ; K. Kristiansen ; E. Willerslev
    Nature Publishing Group (NPG)
    Published 2015
    Staff View
    Publication Date:
    2015-06-13
    Publisher:
    Nature Publishing Group (NPG)
    Print ISSN:
    0028-0836
    Electronic ISSN:
    1476-4687
    Topics:
    Biology
    Chemistry and Pharmacology
    Medicine
    Natural Sciences in General
    Physics
    Keywords:
    Archaeology/methods ; Asia/ethnology ; Asian Continental Ancestry Group/*genetics ; Cultural Evolution/*history ; DNA/genetics/isolation & purification ; Europe/ethnology ; European Continental Ancestry Group/*genetics ; *Fossils ; Gene Frequency/genetics ; Genetics, Population ; Genome, Human/*genetics ; *Genomics ; History, Ancient ; Human Migration/history ; Humans ; Lactose Intolerance/genetics ; Language/*history ; Polymorphism, Single Nucleotide/genetics ; Skin Pigmentation/genetics
    Published by:
    http://www.nature.com/

    Latest Papers from Table of Contents or Articles in Press
  2. 2
    Staff View
    Publication Date:
    2013-08-30
    Publisher:
    Nature Publishing Group (NPG)
    Print ISSN:
    0028-0836
    Electronic ISSN:
    1476-4687
    Topics:
    Biology
    Chemistry and Pharmacology
    Medicine
    Natural Sciences in General
    Physics
    Keywords:
    Adiposity ; Adult ; Bacteria/classification/genetics/*isolation & purification ; Biomarkers/*metabolism ; Body Mass Index ; Case-Control Studies ; Diet ; Dyslipidemias/microbiology ; Energy Metabolism ; Europe/ethnology ; European Continental Ancestry Group ; Female ; Gastrointestinal Tract/*microbiology ; Genes, Bacterial ; Humans ; Inflammation/microbiology ; Insulin Resistance ; Male ; *Metagenome/genetics ; Obesity/metabolism/microbiology ; Overweight/metabolism/microbiology ; Phylogeny ; Thinness/microbiology ; Weight Gain ; Weight Loss
    Published by:
    http://www.nature.com/

    Latest Papers from Table of Contents or Articles in Press
  3. 3
    Staff View
    Publication Date:
    2015-12-04
    Publisher:
    Nature Publishing Group (NPG)
    Print ISSN:
    0028-0836
    Electronic ISSN:
    1476-4687
    Topics:
    Biology
    Chemistry and Pharmacology
    Medicine
    Natural Sciences in General
    Physics
    Keywords:
    Biodiversity ; Diabetes Mellitus, Type 2/drug therapy/*microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/genetics/*physiology ; Humans ; Hypoglycemic Agents/pharmacology/therapeutic use ; Male ; Metagenome/drug effects/physiology ; Metformin/*pharmacology/therapeutic use ; RNA, Ribosomal, 16S/genetics
    Published by:
    http://www.nature.com/

    Latest Papers from Table of Contents or Articles in Press
  4. 4
    Staff View
    Publication Date:
    2013-11-22
    Publisher:
    Nature Publishing Group (NPG)
    Print ISSN:
    0028-0836
    Electronic ISSN:
    1476-4687
    Topics:
    Biology
    Chemistry and Pharmacology
    Medicine
    Natural Sciences in General
    Physics
    Keywords:
    Animals ; Asia/ethnology ; Asian Continental Ancestry Group/*genetics ; Chromosomes, Human, Y/genetics ; DNA, Mitochondrial/genetics ; Emigration and Immigration ; European Continental Ancestry Group/*genetics ; Gene Flow/genetics ; Genome, Human/*genetics ; Genome, Mitochondrial/genetics ; Haplotypes/genetics ; Humans ; Indians, North American/classification/*ethnology/*genetics ; Male ; *Phylogeny ; Phylogeography ; Siberia/ethnology ; Skeleton
    Published by:
    http://www.nature.com/

    Latest Papers from Table of Contents or Articles in Press
  5. 5
    Staff View
    Publication Date:
    2014-02-14
    Publisher:
    Nature Publishing Group (NPG)
    Print ISSN:
    0028-0836
    Electronic ISSN:
    1476-4687
    Topics:
    Biology
    Chemistry and Pharmacology
    Medicine
    Natural Sciences in General
    Physics
    Keywords:
    Archaeology ; Asia/ethnology ; Bone and Bones ; Burial ; Chromosomes, Human, Y/genetics ; DNA, Mitochondrial/genetics ; Emigration and Immigration/history ; Europe/ethnology ; Gene Flow/genetics ; Genome, Human/*genetics ; Haplotypes/genetics ; History, Ancient ; Humans ; Indians, North American/*genetics ; Infant ; Male ; Models, Genetic ; Molecular Sequence Data ; Montana ; *Phylogeny ; Population Dynamics ; Radiometric Dating
    Published by:
    http://www.nature.com/

    Latest Papers from Table of Contents or Articles in Press
  6. 6
    M. Arumugam ; J. Raes ; E. Pelletier ; D. Le Paslier ; T. Yamada ; D. R. Mende ; G. R. Fernandes ; J. Tap ; T. Bruls ; J. M. Batto ; M. Bertalan ; N. Borruel ; F. Casellas ; L. Fernandez ; L. Gautier ; T. Hansen ; M. Hattori ; T. Hayashi ; M. Kleerebezem ; K. Kurokawa ; M. Leclerc ; F. Levenez ; C. Manichanh ; H. B. Nielsen ; T. Nielsen ; N. Pons ; J. Poulain ; J. Qin ; T. Sicheritz-Ponten ; S. Tims ; D. Torrents ; E. Ugarte ; E. G. Zoetendal ; J. Wang ; F. Guarner ; O. Pedersen ; W. M. de Vos ; S. Brunak ; J. Dore ; M. Antolin ; F. Artiguenave ; H. M. Blottiere ; M. Almeida ; C. Brechot ; C. Cara ; C. Chervaux ; A. Cultrone ; C. Delorme ; G. Denariaz ; R. Dervyn ; K. U. Foerstner ; C. Friss ; M. van de Guchte ; E. Guedon ; F. Haimet ; W. Huber ; J. van Hylckama-Vlieg ; A. Jamet ; C. Juste ; G. Kaci ; J. Knol ; O. Lakhdari ; S. Layec ; K. Le Roux ; E. Maguin ; A. Merieux ; R. Melo Minardi ; C. M'Rini ; J. Muller ; R. Oozeer ; J. Parkhill ; P. Renault ; M. Rescigno ; N. Sanchez ; S. Sunagawa ; A. Torrejon ; K. Turner ; G. Vandemeulebrouck ; E. Varela ; Y. Winogradsky ; G. Zeller ; J. Weissenbach ; S. D. Ehrlich ; P. Bork
    Nature Publishing Group (NPG)
    Published 2011
    Staff View
    Publication Date:
    2011-04-22
    Publisher:
    Nature Publishing Group (NPG)
    Print ISSN:
    0028-0836
    Electronic ISSN:
    1476-4687
    Topics:
    Biology
    Chemistry and Pharmacology
    Medicine
    Natural Sciences in General
    Physics
    Keywords:
    Bacteria/*classification/genetics ; Bacterial Typing Techniques ; Biodiversity ; Biomarkers/analysis ; Europe ; Feces/microbiology ; Female ; Humans ; Intestines/*microbiology ; Male ; *Metagenome ; Metagenomics ; Phylogeny
    Published by:
    http://www.nature.com/

    Latest Papers from Table of Contents or Articles in Press
  7. 7
    M. Rasmussen ; X. Guo ; Y. Wang ; K. E. Lohmueller ; S. Rasmussen ; A. Albrechtsen ; L. Skotte ; S. Lindgreen ; M. Metspalu ; T. Jombart ; T. Kivisild ; W. Zhai ; A. Eriksson ; A. Manica ; L. Orlando ; F. M. De La Vega ; S. Tridico ; E. Metspalu ; K. Nielsen ; M. C. Avila-Arcos ; J. V. Moreno-Mayar ; C. Muller ; J. Dortch ; M. T. Gilbert ; O. Lund ; A. Wesolowska ; M. Karmin ; L. A. Weinert ; B. Wang ; J. Li ; S. Tai ; F. Xiao ; T. Hanihara ; G. van Driem ; A. R. Jha ; F. X. Ricaut ; P. de Knijff ; A. B. Migliano ; I. Gallego Romero ; K. Kristiansen ; D. M. Lambert ; S. Brunak ; P. Forster ; B. Brinkmann ; O. Nehlich ; M. Bunce ; M. Richards ; R. Gupta ; C. D. Bustamante ; A. Krogh ; R. A. Foley ; M. M. Lahr ; F. Balloux ; T. Sicheritz-Ponten ; R. Villems ; R. Nielsen ; J. Wang ; E. Willerslev
    American Association for the Advancement of Science (AAAS)
    Published 2011
    Staff View
    Publication Date:
    2011-09-24
    Publisher:
    American Association for the Advancement of Science (AAAS)
    Print ISSN:
    0036-8075
    Electronic ISSN:
    1095-9203
    Topics:
    Biology
    Chemistry and Pharmacology
    Computer Science
    Medicine
    Natural Sciences in General
    Physics
    Keywords:
    African Continental Ancestry Group ; Animals ; Asia ; Asian Continental Ancestry Group/genetics ; Computer Simulation ; DNA, Mitochondrial/genetics ; Emigration and Immigration ; Ethnic Groups/genetics ; European Continental Ancestry Group/genetics ; Far East ; Gene Flow ; Gene Frequency ; Genetics, Population/methods ; *Genome, Human ; Genome, Mitochondrial ; Haplotypes ; Hominidae/genetics ; Humans ; Linkage Disequilibrium ; Male ; Oceanic Ancestry Group/*genetics ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Western Australia
    Published by:
    http://www.aaas.org/

    Latest Papers from Table of Contents or Articles in Press
  8. 8
    L. Orlando ; A. Ginolhac ; G. Zhang ; D. Froese ; A. Albrechtsen ; M. Stiller ; M. Schubert ; E. Cappellini ; B. Petersen ; I. Moltke ; P. L. Johnson ; M. Fumagalli ; J. T. Vilstrup ; M. Raghavan ; T. Korneliussen ; A. S. Malaspinas ; J. Vogt ; D. Szklarczyk ; C. D. Kelstrup ; J. Vinther ; A. Dolocan ; J. Stenderup ; A. M. Velazquez ; J. Cahill ; M. Rasmussen ; X. Wang ; J. Min ; G. D. Zazula ; A. Seguin-Orlando ; C. Mortensen ; K. Magnussen ; J. F. Thompson ; J. Weinstock ; K. Gregersen ; K. H. Roed ; V. Eisenmann ; C. J. Rubin ; D. C. Miller ; D. F. Antczak ; M. F. Bertelsen ; S. Brunak ; K. A. Al-Rasheid ; O. Ryder ; L. Andersson ; J. Mundy ; A. Krogh ; M. T. Gilbert ; K. Kjaer ; T. Sicheritz-Ponten ; L. J. Jensen ; J. V. Olsen ; M. Hofreiter ; R. Nielsen ; B. Shapiro ; J. Wang ; E. Willerslev
    Nature Publishing Group (NPG)
    Published 2013
    Staff View
    Publication Date:
    2013-06-28
    Publisher:
    Nature Publishing Group (NPG)
    Print ISSN:
    0028-0836
    Electronic ISSN:
    1476-4687
    Topics:
    Biology
    Chemistry and Pharmacology
    Medicine
    Natural Sciences in General
    Physics
    Keywords:
    Animals ; Conservation of Natural Resources ; DNA/analysis/genetics ; Endangered Species ; Equidae/classification/genetics ; *Evolution, Molecular ; Fossils ; Genetic Variation/genetics ; Genome/*genetics ; History, Ancient ; Horses/classification/*genetics ; *Phylogeny ; Proteins/analysis/chemistry/genetics ; Yukon Territory
    Published by:
    http://www.nature.com/

    Latest Papers from Table of Contents or Articles in Press
  9. 9
    Staff View
    Publication Date:
    2018-07-10
    Publisher:
    The American Association of Immunologists (AAI)
    Print ISSN:
    0022-1767
    Electronic ISSN:
    1550-6606
    Topics:
    Medicine
    Published by:
    http://www.aai.org/

    Latest Papers from Table of Contents or Articles in Press
  10. 10
    Lamberth, K. ; Nielsen, M. ; Lundegaard, C. ; Worning, P. ; Laurmøller, S. L. ; Lund, O. ; Brunak, S. ; Buus, S.

    Oxford, UK; Malden, USA : Blackwell Science Ltd/Inc.
    Published 2004
    Staff View
    ISSN:
    1365-3083
    Source:
    Blackwell Publishing Journal Backfiles 1879-2005
    Topics:
    Medicine
    Notes:
    Rationale:  We have previously demonstrated that bioinformatics tools such as artificial neural networks (ANNs) are capable of performing pathogen-, genome- and HLA-wide predictions of peptide–HLA interactions. These tools may therefore enable a fast and rational approach to epitope identification and thereby assist in the development of vaccines and immunotherapy. A crucial step in the generation of such bioinformatics tools is the selection of data representing the event in question (in casu peptide–HLA interaction). This is particularly important when it is difficult and expensive to obtain data. Herein, we demonstrate the importance in selecting information-rich data and we develop a computational method, query-by-committee, which can perform a global identification of such information-rich data in an unbiased and automated manner. Furthermore, we demonstrate how this method can be applied to an efficient iterative development strategy for these bioinformatics tools.Methods:  A large panel of binding affinities of peptides binding to HLA A*0204 was measured by a radioimmunoassay (RIA). This data was used to develop multiple first generation ANNs, which formed a virtual committee. This committee was used to screen (or ‘queried’) for peptides, where the ANNs agreed (‘low-QBC’), or disagreed (‘high-QBC’), on their HLA-binding potential. Seventeen low-QBC peptides and 17 high-QBC peptides were synthesized and tested. The high- or low-QBC data were added to the original data, and new high- or low-QBC second generation ANNs were developed, respectively. This procedure was repeated 40 times.Results:  The high-QBC-enriched ANN performed significantly better than the low-QBC-enriched ANN in 37 of the 40 tests.Conclusion:  These results demonstrate that high-QBC-enriched networks perform better than low-QBC-enriched networks in selecting informative data for developing peptide–MHC-binding predictors. This improvement in selecting data is not due to differences in network training performance but due to the difference in information content in the high-QBC experiment and in the low-QBC experiment. Finally, it should be noted that this strategy could be used in many contexts where generation of data is difficult and costly.
    Type of Medium:
    Electronic Resource
    URL:
    http://dx.doi.org/10.1111/j.0300-9475.2004.01423bf.x

    Articles: DFG German National Licenses
  11. 11
    Sylvester-Hvid, C. ; Nielsen, M. ; Lamberth, K. ; Røder, G. ; Justesen, S. ; Lundegaard, C. ; Worning, P. ; Thomadsen, H. ; Lund, O. ; Brunak, S. ; Buus, S.

    Oxford, UK; Malden, USA : Blackwell Science Ltd/Inc.
    Published 2004
    Staff View
    ISSN:
    1365-3083
    Source:
    Blackwell Publishing Journal Backfiles 1879-2005
    Topics:
    Medicine
    Notes:
    An effective SARS vaccine is likely to include components that can induce specific cytotoxic T-cell (CTL) responses. The specificities of such responses are governed by HLA-restricted presentation of SARS-derived peptide epitopes. Exact knowledge of how the immune system handles protein antigens would allow for the identification of such linear sequences directly from genomic/proteomic sequence information. The latter was recently established when a causative coronavirus (SARS CoV) was isolated and full-length sequenced. Here, we have combined advanced bioinformatics and high-throughput immunology to perform an HLA supertype, genome-wide scan for SARS-specific cytotoxic T cell epitopes. The scan includes all nine human HLA supertypes in total covering 〉99% of all major human populations. For each HLA supertype, we have selected the 15 top candidates for test in biochemical-binding assays. At this time (approximately 6 months after the genome was established), we have tested the majority of the HLA supertypes and identified almost 100 potential vaccine candidates. These should be further validated in SARS survivors and used for vaccine formulation. We suggest that immunobioinformatics may become a fast and valuable tool in rational vaccine design.
    Type of Medium:
    Electronic Resource
    URL:
    http://dx.doi.org/10.1111/j.0300-9475.2004.01423bd.x

    Articles: DFG German National Licenses
  12. 12
    Petersen, T. R. ; Buus, S. ; Brunak, S. ; Nissen, M. H. ; Sherman, L. A. ; Claesson, M. H.

    Oxford, UK : Blackwell Science Ltd
    Published 2001
    Staff View
    ISSN:
    1365-3083
    Source:
    Blackwell Publishing Journal Backfiles 1879-2005
    Topics:
    Medicine
    Notes:
    The replacement of a suboptimal amino acid in a primary anchor position with an optimal residue improves human leucocyte antigen (HLA) binding and immunogenicity, while maintaining cytotoxic T lymphocyte (CTL) specificity. Using a neural network capable of performing quantitative predictions of peptide binding to HLA-A2 molecules, we identified three p53 protein-derived nonamer peptides with intermediate binding owing to suboptimal amino acids in the P2 anchor position. These peptides were synthesized along with the corresponding analogs, where the natural P2 residue had been replaced with the optimal leucine residue. All three modified peptides bound to and more efficiently stabilized HLA-A2 molecules than the corresponding nonmodified peptides. The HLA-A2 transgenic mice were used for immunization. Two of the epitopes were more immunogenic in their modified than in their natural versions. The CTLs raised against the modified peptides efficiently killed the target cells pulsed with the corresponding native peptide. In terms of sensitizing the targets cells for the CTL killing, the modified peptides were more efficient than native peptides. Finally, the CTLs induced by modified peptide killed HLA-A2 transgenic mouse fibrosarcoma cells transfected with human p53 DNA. The data suggest that modified self-peptides derived from overexpressed tumour-associated proteins can be used in vaccine development against cancer, and that quantitative predictions of HLA binding is of value in the rational selection and improvement of target epitopes recognized by CTLs.
    Type of Medium:
    Electronic Resource
    URL:
    http://dx.doi.org/10.1046/j.1365-3083.2001.00887.x

    Articles: DFG German National Licenses
  13. 13
    Staff View
    ISSN:
    0014-5793
    Keywords:
    Binary distance matrix ; Neural network ; Protein secondary structure prediction ; Protein tertiary structure prediction ; Steepest descent minimization
    Source:
    Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics:
    Biology
    Chemistry and Pharmacology
    Physics
    Type of Medium:
    Electronic Resource
    URL:
    http://linkinghub.elsevier.com/retrieve/pii/0014-5793(90)80632-S

    Articles: DFG German National Licenses
  14. 14
    Staff View
    ISSN:
    0022-2836
    Keywords:
    distance inequalities ; distance matrix ; distance threshold ; protein folding ; root-mean-square
    Source:
    Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics:
    Biology
    Type of Medium:
    Electronic Resource
    URL:
    http://dx.doi.org/10.1006/jmbi.1993.1332

    Articles: DFG German National Licenses
  15. 15
    Staff View
    ISSN:
    0022-2836
    Keywords:
    genetic code ; hydrophobicity ; neural network
    Source:
    Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics:
    Biology
    Type of Medium:
    Electronic Resource
    URL:
    http://dx.doi.org/10.1006/jmbi.1994.1683

    Articles: DFG German National Licenses
  16. 16
    Staff View
    ISSN:
    0014-5793
    Keywords:
    Neural network ; Perceptron ; Protein folding ; Protein homology ; Rhodopsin α-helix ; Secondary structure
    Source:
    Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics:
    Biology
    Chemistry and Pharmacology
    Physics
    Type of Medium:
    Electronic Resource
    URL:
    http://linkinghub.elsevier.com/retrieve/pii/0014-5793(88)81066-4

    Articles: DFG German National Licenses
  17. 17
    Staff View
    ISSN:
    0167-7799
    Source:
    Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics:
    Biology
    Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium:
    Electronic Resource
    URL:
    http://linkinghub.elsevier.com/retrieve/pii/0167-7799(90)90206-D

    Articles: DFG German National Licenses
  18. 18
    Bohr, H. ; Brunak, S. ; Bohr, J.

    New York, NY [u.a.] : Wiley-Blackwell
    Published 1997
    Staff View
    ISSN:
    0197-8462
    Keywords:
    DNA ; hydrolysis ; linking ; microwaves ; protein ; Life and Medical Sciences ; Occupational Health and Environmental Toxicology
    Source:
    Wiley InterScience Backfile Collection 1832-2000
    Topics:
    Biology
    Physics
    Notes:
    It is shown that the eigenfrequency of collective twist excitations in chain molecules can be in the megahertz and gigahertz range. Accordingly, resonance states can be obtained at specific frequencies, and phenomena that involve structural properties can take place. Chain molecules can alter their conformation and their ability to function, and a breaking of the chain can result. It is suggested that this phenomenon forms the basis for effects caused by the interaction of microwaves and biomolecules, e.g., microwave assisted hydrolysis of chain molecules. Bioelectromagnetics 18:187-189, 1997. © 1997 Wiley-Liss, Inc.
    Additional Material:
    1 Ill.
    Type of Medium:
    Electronic Resource

    Articles: DFG German National Licenses