94
F. Cheng
48. Cheng F, Desai RJ, Handy DE, Wang R, Schneeweiss S, Barabasi AL et al (2018) Networkbased approach to prediction and population-based validation of in silico drug repurposing.
Nat Commun 9(1):2691
49. Lu W, Yao X, Ouyang P, Dong N, Wu D, Jiang X et al (2017) Drug repurposing of histone deacetylase inhibitors that alleviate neutrophilic inflammation in acute lung injury and
idiopathic pulmonary fibrosis via inhibiting leukotriene A4 hydrolase and blocking LTB4
biosynthesis. J Med Chem 60(5):1817–1828
50. Cheng F, Murray JL, Zhao J, Sheng J, Zhao Z, Rubin DH (2016) Systems biology-based
investigation of cellular antiviral drug targets identified by gene-trap insertional mutagenesis.
PLoS Comput Biol 12(9):e1005074
51. Cheng F, Murray JL, Rubin DH (2016) Drug repurposing, new treatments for Zika virus
infection? Trends Mol Med 22(11):919–921
52. Cai C, Fang J, Guo P, Wang Q, Hong H, Moslehi J et al (2018) In silico pharmacoepidemiologic
evaluation of drug-induced cardiovascular complications using combined classifiers. J Chem
Inf Model 58(5):943–956
53. Law V, Knox C, Djoumbou Y, Jewison T, Guo AC, Liu Y et al (2014) DrugBank 4.0, shedding
new light on drug metabolism. Nucleic Acids Res 42(Database issue):D1091–1097
54. Yang H, Qin C, Li YH, Tao L, Zhou J, Yu CY et al (2016) Therapeutic target database update
2016, enriched resource for bench to clinical drug target and targeted pathway information.
Nucleic Acids Res 44(D1):D1069–D1074
55. Hernandez-Boussard T, Whirl-Carrillo M, Hebert JM, Gong L, Owen R, Gong M et al (2008)
The pharmacogenetics and pharmacogenomics knowledge base, accentuating the knowledge.
Nucleic Acids Res 36(Database issue):D913–918
56. Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A et al (2012) ChEMBL, a
large-scale bioactivity database for drug discovery. Nucleic Acids Res 40(D1):D1100–D1107
57. Liu TQ, Lin YM, Wen X, Jorissen RN, Gilson MK (2007) BindingDB, a web-accessible
database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res
35:D198–D201
58. Pawson AJ, Sharman JL, Benson HE, Faccenda E, Alexander SPH, Buneman OP et al (2014)
The IUPHAR/BPS Guide to PHARMACOLOGY, an expert-driven knowledgebase of drug
targets and their ligands. Nucleic Acids Res 42(D1):D1098–D1106
59. Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S et al (2004) UniProt,
the universal protein knowledgebase. Nucleic Acids Res 32:D115–D119
60. Rolland T, Tasan M, Charloteaux B, Pevzner SJ, Zhong Q, Sahni N et al (2014) A proteomescale map of the human interactome network. Cell 159(5):1212–1226
61. Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N et al (2005)
Towards a proteome-scale map of the human protein-protein interaction network. Nature
437(7062):1173–1178
62. Mosca R, Ceol A, Aloy P (2013) Interactome3D, adding structural details to protein networks.
Nat Methods 10(1):47–53
63. Meyer MJ, Das J, Wang X, Yu H (2013) INstruct, a database of high-quality 3D structurally
resolved protein interactome networks. Bioinformatics 29(12):1577–1579
64. Meyer MJ, Beltran JF, Liang S, Fragoza R, Rumack A, Liang J et al (2018) Interactome
INSIDER, a structural interactome browser for genomic studies. Nat Methods 15(2):107–114
65. Cheng F, Jia P, Wang Q, Zhao Z (2014) Quantitative network mapping of the human kinome
interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer
therapy. Oncotarget 5(11):3697–3710
66. Peri S, Navarro JD, Kristiansen TZ, Amanchy R, Surendranath V, Muthusamy B et al (2004)
Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res
32(Database issue):D497–501
67. Newman RH, Hu J, Rho HS, Xie Z, Woodard C, Neiswinger J et al (2013) Construction of
human activity-based phosphorylation networks. Mol Syst Biol 9:655
68. Hu J, Rho HS, Newman RH, Zhang J, Zhu H, Qian J (2014) PhosphoNetworks, a database
for human phosphorylation networks. Bioinformatics 30(1):141–142
F. Cheng
48. Cheng F, Desai RJ, Handy DE, Wang R, Schneeweiss S, Barabasi AL et al (2018) Networkbased approach to prediction and population-based validation of in silico drug repurposing.
Nat Commun 9(1):2691
49. Lu W, Yao X, Ouyang P, Dong N, Wu D, Jiang X et al (2017) Drug repurposing of histone deacetylase inhibitors that alleviate neutrophilic inflammation in acute lung injury and
idiopathic pulmonary fibrosis via inhibiting leukotriene A4 hydrolase and blocking LTB4
biosynthesis. J Med Chem 60(5):1817–1828
50. Cheng F, Murray JL, Zhao J, Sheng J, Zhao Z, Rubin DH (2016) Systems biology-based
investigation of cellular antiviral drug targets identified by gene-trap insertional mutagenesis.
PLoS Comput Biol 12(9):e1005074
51. Cheng F, Murray JL, Rubin DH (2016) Drug repurposing, new treatments for Zika virus
infection? Trends Mol Med 22(11):919–921
52. Cai C, Fang J, Guo P, Wang Q, Hong H, Moslehi J et al (2018) In silico pharmacoepidemiologic
evaluation of drug-induced cardiovascular complications using combined classifiers. J Chem
Inf Model 58(5):943–956
53. Law V, Knox C, Djoumbou Y, Jewison T, Guo AC, Liu Y et al (2014) DrugBank 4.0, shedding
new light on drug metabolism. Nucleic Acids Res 42(Database issue):D1091–1097
54. Yang H, Qin C, Li YH, Tao L, Zhou J, Yu CY et al (2016) Therapeutic target database update
2016, enriched resource for bench to clinical drug target and targeted pathway information.
Nucleic Acids Res 44(D1):D1069–D1074
55. Hernandez-Boussard T, Whirl-Carrillo M, Hebert JM, Gong L, Owen R, Gong M et al (2008)
The pharmacogenetics and pharmacogenomics knowledge base, accentuating the knowledge.
Nucleic Acids Res 36(Database issue):D913–918
56. Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A et al (2012) ChEMBL, a
large-scale bioactivity database for drug discovery. Nucleic Acids Res 40(D1):D1100–D1107
57. Liu TQ, Lin YM, Wen X, Jorissen RN, Gilson MK (2007) BindingDB, a web-accessible
database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res
35:D198–D201
58. Pawson AJ, Sharman JL, Benson HE, Faccenda E, Alexander SPH, Buneman OP et al (2014)
The IUPHAR/BPS Guide to PHARMACOLOGY, an expert-driven knowledgebase of drug
targets and their ligands. Nucleic Acids Res 42(D1):D1098–D1106
59. Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S et al (2004) UniProt,
the universal protein knowledgebase. Nucleic Acids Res 32:D115–D119
60. Rolland T, Tasan M, Charloteaux B, Pevzner SJ, Zhong Q, Sahni N et al (2014) A proteomescale map of the human interactome network. Cell 159(5):1212–1226
61. Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N et al (2005)
Towards a proteome-scale map of the human protein-protein interaction network. Nature
437(7062):1173–1178
62. Mosca R, Ceol A, Aloy P (2013) Interactome3D, adding structural details to protein networks.
Nat Methods 10(1):47–53
63. Meyer MJ, Das J, Wang X, Yu H (2013) INstruct, a database of high-quality 3D structurally
resolved protein interactome networks. Bioinformatics 29(12):1577–1579
64. Meyer MJ, Beltran JF, Liang S, Fragoza R, Rumack A, Liang J et al (2018) Interactome
INSIDER, a structural interactome browser for genomic studies. Nat Methods 15(2):107–114
65. Cheng F, Jia P, Wang Q, Zhao Z (2014) Quantitative network mapping of the human kinome
interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer
therapy. Oncotarget 5(11):3697–3710
66. Peri S, Navarro JD, Kristiansen TZ, Amanchy R, Surendranath V, Muthusamy B et al (2004)
Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res
32(Database issue):D497–501
67. Newman RH, Hu J, Rho HS, Xie Z, Woodard C, Neiswinger J et al (2013) Construction of
human activity-based phosphorylation networks. Mol Syst Biol 9:655
68. Hu J, Rho HS, Newman RH, Zhang J, Zhu H, Qian J (2014) PhosphoNetworks, a database
for human phosphorylation networks. Bioinformatics 30(1):141–142