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Large-scale data and text mining

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    1. Large-scale data and text mining Lars Juhl Jensen
    2.  
    3.  
    4. function prediction
    5. Jensen, Gupta et al., Journal of Molecular Biology , 2002
    6.  
    7.  
    8. cell-cycle regulation
    9. de Lichtenberg, Jensen et al., Science , 2005
    10. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
    11. phosphorylation
    12.  
    13. signaling networks
    14. upstream events
    15. downstream events
    16. NetworKIN
    17.  
    18. sequence motifs
    19. NetPhorest
    20. automated pipeline
    21. Miller, Jensen et al., Science Signaling , 2008
    22. data organization
    23. Miller, Jensen et al., Science Signaling , 2008
    24. compilation of datasets
    25. redundancy reduction
    26. training and evaluation
    27. motif atlas
    28.  
    29. model organisms
    30. other modifications
    31. protein networks
    32. functional associations
    33.  
    34. STRING
    35. Jensen, Kuhn et al., Nucleic Acids Research , 2009
    36. 630 genomes
    37. genomic context
    38. Korbel et al., Nature Biotechnology , 2004
    39. Korbel et al., Nature Biotechnology , 2004
    40. Korbel et al., Nature Biotechnology , 2004
    41. physical interactions
    42. Jensen & Bork, Science , 2008
    43. genetic interactions
    44. Beyer et al., Nature Reviews Genetics , 2007
    45. gene coexpression
    46.  
    47. curated knowledge
    48. Letunic & Bork, Trends in Biochemical Sciences , 2008
    49. literature mining
    50. >10 km
    51.  
    52. confidence scores
    53. cross-species integration
    54. visualization
    55. Frishman et al., Modern Genome Annotation , 2009
    56. small molecules
    57. STITCH
    58. Kuhn et al., Nucleic Acids Research , 2008
    59. kinase inhibitor screens
    60. Fedorov et al., PNAS , 2007
    61. new targets for old drugs
    62. chemical similarity
    63. Campillos & Kuhn et al., Science , 2008
    64. side-effect similarity
    65. information on side effects
    66. package inserts
    67. Campillos, Kuhn et al., Science , 2008
    68. text mining
    69. side-effect ontology
    70. Campillos, Kuhn et al., Science , 2008
    71. side-effect correlations
    72. Campillos, Kuhn et al., Science , 2008
    73. side-effect frequencies
    74. Campillos & Kuhn et al., Science , 2008
    75. combined similarity score
    76. Campillos, Kuhn et al., Science , 2008
    77. thousands of predictions
    78. categorization
    79. Campillos, Kuhn et al., Science , 2008
    80. 20 drug–drug relations
    81. Campillos, Kuhn et al., Science , 2008
    82. in vitro binding assays
    83. K i <10 µM for 11 of 20
    84. cell assays
    85. 9 of 9 showed activity
    86. augmented browsing
    87. Reflect
    88.  
    89. collaborate publishers
    90.  
    91. Acknowledgments
      • NetPhorest.info
        • Rune Linding
        • Martin Lee Miller
        • Francesca Diella
        • Claus Jørgensen
        • Michele Tinti
        • Lei Li
        • Marilyn Hsiung
        • Sirlester A. Parker
        • Jennifer Bordeaux
        • Thomas Sicheritz-Pontén
        • Marina Olhovsky
        • Adrian Pasculescu
        • Jes Alexander
        • Stefan Knapp
        • Nikolaj Blom
        • Peer Bork
        • Shawn Li
        • Gianni Cesareni
        • Tony Pawson
        • Benjamin E. Turk
        • Michael B. Yaffe
        • Søren Brunak
      • STRING-DB.org
        • Christian von Mering
        • Michael Kuhn
        • Manuel Stark
        • Samuel Chaffron
        • Chris Creevey
        • Jean Muller
        • Tobias Doerks
        • Philippe Julien
        • Alexander Roth
        • Milan Simonovic
        • Jan Korbel
        • Berend Snel
        • Martijn Huynen
        • Peer Bork
        • STITCH-DB.org
        • Michael Kuhn
        • Damian Szklarczyk
        • Andrea Franceschini
        • Monica Campillos
        • Christian von Mering
        • Lars Juhl Jensen
        • Andreas Beyer
        • Peer Bork
      • NetworKIN.info
        • Rune Linding
        • Gerard Ostheimer
        • Heiko Horn
        • Martin Lee Miller
        • Francesca Diella
        • Karen Colwill
        • Jing Jin
        • Pavel Metalnikov
        • Vivian Nguyen
        • Adrian Pasculescu
        • Jin Gyoon Park
        • Leona D. Samson
        • Rob Russell
        • Peer Bork
        • Michael Yaffe
        • Tony Pawson
        • Reflect.ws
        • Sean O’Donoghue
        • Heiko Horn
        • Evangelos Pafilis
        • Michael Kuhn
        • Nigel Brown
        • Reinhardt Schneider
    92. larsjuhljensen

    + Lars Juhl JensenLars Juhl Jensen, 1 month ago

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