-
1
-
-
84857743319
-
Diagnosing the decline in pharmaceutical R&D efficiency
-
Scannell, J.W., Blanckley, A., Boldon, H., Warrington, B. Diagnosing the decline in pharmaceutical R&D efficiency. Nat. Rev. Drug Discov. 2012,11,191-200.
-
(2012)
Nat. Rev. Drug Discov.
, vol.11
, pp. 191-200
-
-
Scannell, J.W.1
Blanckley, A.2
Boldon, H.3
Warrington, B.4
-
2
-
-
84990854138
-
The Importance of Clinical Trials in Drug Development
-
Akhondzadeh, S. The Importance of Clinical Trials in Drug Development. Avicenna J. Med. Biotechnol. 2016, 8,151.
-
(2016)
Avicenna J. Med. Biotechnol.
, vol.8
, pp. 151
-
-
Akhondzadeh, S.1
-
3
-
-
84881315517
-
Validating therapeutic targets through human genetics
-
Plenge, R.M., Scolnick, E.M., Altshuler, D. Validating therapeutic targets through human genetics. Nat. Rev. Drug Discov. 2013,12, 581-594.
-
(2013)
Nat. Rev. Drug Discov.
, vol.12
, pp. 581-594
-
-
Plenge, R.M.1
Scolnick, E.M.2
Altshuler, D.3
-
4
-
-
4344645978
-
Can the pharmaceutical industry reduce attrition rates?
-
Kola, I., Landis, J. Can the pharmaceutical industry reduce attrition rates? Nat. Rev. Drug Discov. 2004, 3,1-5.
-
(2004)
Nat. Rev. Drug Discov.
, vol.3
, pp. 1-5
-
-
Kola, I.1
Landis, J.2
-
5
-
-
77649234756
-
Productivity: The pharmaceutical industry's grand challenge
-
Paul, S.M., Mytelka, D.S., Dunwiddie, C.T., Persinger, C.C., Munos, B.H., Lindborg, S.R., Schacht, A.L. How to improve RD productivity: The pharmaceutical industry's grand challenge. Nat. Rev. Drug Discov. 2010, 9, 203-214.
-
(2010)
Nat. Rev. Drug Discov.
, vol.9
, pp. 203-214
-
-
Paul, S.M.1
Mytelka, D.S.2
Dunwiddie, C.T.3
Persinger, C.C.4
Munos, B.H.5
Lindborg, S.R.6
Schacht, A.L.7
How To Improve, R.D.8
-
6
-
-
2442465034
-
Opinion/Outlook: Prospects for productivity
-
Booth, B., Zemmel, R. Opinion/Outlook: Prospects for productivity. Nat. Rev. Drug Discov. 2004, 3,451-456.
-
(2004)
Nat. Rev. Drug Discov.
, vol.3
, pp. 451-456
-
-
Booth, B.1
Zemmel, R.2
-
7
-
-
4344668661
-
Drug repositioning: Identifying and developing new uses for existing drugs
-
Ashburn, T.T., Thor, K.B. Drug repositioning: Identifying and developing new uses for existing drugs. Nat. Rev. Drug Discov. 2004, 3, 673-683.
-
(2004)
Nat. Rev. Drug Discov.
, vol.3
, pp. 673-683
-
-
Ashburn, T.T.1
Thor, K.B.2
-
8
-
-
84893675072
-
The year's new drugs & biologics
-
Graul, A.I., Cruces, E., Stringer, M. The year's new drugs & biologics, 2013: Part I. Drugs of Today 2014, 50, 51-100.
-
(2013)
Part I. Drugs of Today
, vol.50
, pp. 51-100
-
-
Graul, A.I.1
Cruces, E.2
Stringer, M.3
-
9
-
-
84875459651
-
Computational drug repositioning: From data to therapeutics
-
Hurle, M.R., Yang, L., Xie, Q., Rajpal, D.K., Sanseau, P., Agarwal, P. Computational drug repositioning: From data to therapeutics. Clin. Pharmacol. Ther. 2013, 93, 335-341.
-
(2013)
Clin. Pharmacol. Ther.
, vol.93
, pp. 335-341
-
-
Hurle, M.R.1
Yang, L.2
Xie, Q.3
Rajpal, D.K.4
Sanseau, P.5
Agarwal, P.6
-
10
-
-
85044646894
-
Inventing new therapies without reinventing the wheel: The power of drug repurposing
-
Papapetropoulos, A., Szabo, C. Inventing new therapies without reinventing the wheel: The power of drug repurposing. Br. J. Pharmacol. 2018, 2016-2018.
-
(2018)
Br. J. Pharmacol.
, pp. 2016-2018
-
-
Papapetropoulos, A.1
Szabo, C.2
-
11
-
-
80052218993
-
Drug repositioning: Re-investigating existing drugs for new therapeutic indications
-
Padhy, B.M., Gupta, Y.K. Drug repositioning: Re-investigating existing drugs for new therapeutic indications. J. Postgrad. Med. 2011, 57,153-160.
-
(2011)
J. Postgrad. Med.
, vol.57
, pp. 153-160
-
-
Padhy, B.M.1
Gupta, Y.K.2
-
12
-
-
84975795401
-
Can you teach old drugs new tricks?
-
Nosengo, N. Can you teach old drugs new tricks? Nature 2016, 534, 314-316.
-
(2016)
Nature
, vol.534
, pp. 314-316
-
-
Nosengo, N.1
-
13
-
-
79960775459
-
Drug repositioning for orphan diseases
-
Sardana, D., Zhu, C., Zhang, M., Gudivada, R.C., Yang, L., Jegga, A.G. Drug repositioning for orphan diseases. Brief. Bioinform. 2011,12, 346-356.
-
(2011)
Brief. Bioinform.
, vol.12
, pp. 346-356
-
-
Sardana, D.1
Zhu, C.2
Zhang, M.3
Gudivada, R.C.4
Yang, L.5
Jegga, A.G.6
-
14
-
-
85019946189
-
Drug repurposing from the perspective of pharmaceutical companies
-
Cha, Y., Erez, T., Reynolds, I.J., Kumar, D., Ross, J., Koytiger, G., Kusko, R., Zeskind, B., Risso, S., Kagan, E., et al. Drug repurposing from the perspective of pharmaceutical companies. Br. J. Pharmacol. 2017.
-
(2017)
Br. J. Pharmacol
-
-
Cha, Y.1
Erez, T.2
Reynolds, I.J.3
Kumar, D.4
Ross, J.5
Koytiger, G.6
Kusko, R.7
Zeskind, B.8
Risso, S.9
Kagan, E.10
-
15
-
-
84960079810
-
A survey of current trends in computational drug repositioning
-
Li, J., Zheng, S., Chen, B., Butte, A.J., Swamidass, S.J., Lu, Z. A survey of current trends in computational drug repositioning. Brief. Bioinform. 2016,17, 2-12.
-
(2016)
Brief. Bioinform.
, vol.17
, pp. 2-12
-
-
Li, J.1
Zheng, S.2
Chen, B.3
Butte, A.J.4
Swamidass, S.J.5
Lu, Z.6
-
16
-
-
84959523909
-
Systems Biology Approaches to a Rational Drug Discovery Paradigm
-
Prathipati, P., Mizuguchi, K. Systems Biology Approaches to a Rational Drug Discovery Paradigm. Curr. Top. Med. Chem. 2015,16,1009-1025.
-
(2015)
Curr. Top. Med. Chem.
, vol.16
, pp. 1009-1025
-
-
Prathipati, P.1
Mizuguchi, K.2
-
17
-
-
84858978535
-
Drug repositioning for personalized medicine
-
Li, Y.Y., Jones, S.J.M. Drug repositioning for personalized medicine. Genome Med. 2012, 4, 27.
-
(2012)
Genome Med.
, vol.4
, pp. 27
-
-
Li, Y.Y.1
Jones, S.J.M.2
-
18
-
-
84901357361
-
Toward better drug repositioning: Prioritizing and integrating existing methods into efficient pipelines
-
Jin, G., Wong, S.T.C. Toward better drug repositioning: Prioritizing and integrating existing methods into efficient pipelines. Drug Discov. Today 2014,19, 637-644.
-
(2014)
Drug Discov. Today
, vol.19
, pp. 637-644
-
-
Jin, G.1
Wong, S.T.C.2
-
19
-
-
84873076688
-
In silico drug repositioning: What we need to know
-
Liu, Z., Fang, H., Reagan, K., Xu, X., Mendrick, D.L., Slikker, W., Tong, W. In silico drug repositioning: What we need to know. Drug Discov. Today 2013,18,110-115.
-
(2013)
Drug Discov. Today
, vol.18
, pp. 110-115
-
-
Liu, Z.1
Fang, H.2
Reagan, K.3
Xu, X.4
Mendrick, D.L.5
Slikker, W.6
Tong, W.7
-
20
-
-
84875963165
-
Drug Target Prediction and Repositioning Using an Integrated Network-Based Approach
-
Emig, D., Ivliev, A., Pustovalova, O., Lancashire, L., Bureeva, S., Nikolsky, Y., Bessarabova, M. Drug Target Prediction and Repositioning Using an Integrated Network-Based Approach. PLoS ONE 2013, 8.
-
(2013)
Plos ONE
, pp. 8
-
-
Emig, D.1
Ivliev, A.2
Pustovalova, O.3
Lancashire, L.4
Bureeva, S.5
Nikolsky, Y.6
Bessarabova, M.7
-
21
-
-
84863695210
-
Prediction of drug-target interactions and drug repositioning via network-based inference
-
Cheng, F., Liu, C., Jiang, J., Lu, W., Li, W., Liu, G., Zhou, W., Huang, J., Tang, Y. Prediction of drug-target interactions and drug repositioning via network-based inference. PLoS Comput. Biol. 2012, 8.
-
(2012)
Plos Comput. Biol.
, pp. 8
-
-
Cheng, F.1
Liu, C.2
Jiang, J.3
Lu, W.4
Li, W.5
Liu, G.6
Zhou, W.7
Huang, J.8
Tang, Y.9
-
22
-
-
77955628292
-
Network-based relating pharmacological and genomic spaces for drug target identification
-
Zhao, S., Li, S. Network-based relating pharmacological and genomic spaces for drug target identification. PLoS ONE 2010, 5.
-
(2010)
Plos ONE
, pp. 5
-
-
Zhao, S.1
Li, S.2
-
23
-
-
83755163958
-
Systematic drug repositioning based on clinical side-effects
-
Yang, L., Agarwal, P. Systematic drug repositioning based on clinical side-effects. PLoS ONE 2011, 6.
-
(2011)
Plos ONE
, pp. 6
-
-
Yang, L.1
Agarwal, P.2
-
24
-
-
68249144628
-
Drug discovery using chemical systems biology: Repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis
-
Kinnings, S.L., Liu, N., Buchmeier, N., Tonge, P.J., Xie, L., Bourne, P.E. Drug discovery using chemical systems biology: Repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis. PLoS Comput. Biol.2009, 5.
-
(2009)
Plos Comput. Biol
, pp. 5
-
-
Kinnings, S.L.1
Liu, N.2
Buchmeier, N.3
Tonge, P.J.4
Xie, L.5
Bourne, P.E.6
-
25
-
-
85009423948
-
A Systematic Framework for Drug Repositioning from Integrated Omics and Drug Phenotype Profiles Using Pathway-Drug Network
-
Jadamba, E., Shin, M. A Systematic Framework for Drug Repositioning from Integrated Omics and Drug Phenotype Profiles Using Pathway-Drug Network. BioMed Res. Int. 2016, 2016.
-
(2016)
Biomed Res. Int.
, pp. 2016
-
-
Jadamba, E.1
Shin, M.2
-
26
-
-
84886775358
-
Pathway-based drug repositioning using causal inference
-
Li, J., Lu, Z. Pathway-based drug repositioning using causal inference. BMC Bioinform. 2013,14.
-
(2013)
BMC Bioinform.
, pp. 14
-
-
Li, J.1
Lu, Z.2
-
27
-
-
77953682031
-
Computational approaches for drug repositioning and combination therapy design
-
Kotelnikova, E., Yuryev, A., Mazo, I., Daraselia, N. Computational approaches for drug repositioning and combination therapy design. J. Bioinform. Comput. Biol. 2010, 8, 593-606.
-
(2010)
J. Bioinform. Comput. Biol.
, vol.8
, pp. 593-606
-
-
Kotelnikova, E.1
Yuryev, A.2
Mazo, I.3
Daraselia, N.4
-
28
-
-
84862777666
-
ApoE-Directed Therapeutics Rapidly Clear beta-Amyloid and Reverse Deficits in AD Mouse Models
-
Cramer, P., Cirrito, J., Wesson, D. ApoE-Directed Therapeutics Rapidly Clear beta-Amyloid and Reverse Deficits in AD Mouse Models. Science 2012, 335,1503-1506.
-
(2012)
Science
, vol.335
, pp. 1503-1506
-
-
Cramer, P.1
Cirrito, J.2
Wesson, D.3
-
29
-
-
34147108307
-
Pathway Analysis for Design of Promiscuous Drugs and Selective Drug Mixtures
-
Sivachenko, A., Kalinin, A., Yuryev, A. Pathway Analysis for Design of Promiscuous Drugs and Selective Drug Mixtures. Curr. Drug Discov. Technol. 2006, 3, 269-277.
-
(2006)
Curr. Drug Discov. Technol.
, vol.3
, pp. 269-277
-
-
Sivachenko, A.1
Kalinin, A.2
Yuryev, A.3
-
30
-
-
84858770007
-
Old drug, new hope for Alzheimer's disease
-
Strittmatter, W.J. Old drug, new hope for Alzheimer's disease. Science 2012, 335, 1447-1448.
-
(2012)
Science
, vol.335
, pp. 1447-1448
-
-
Strittmatter, W.J.1
-
31
-
-
79959473110
-
An enhanced Petri-Net model to predict synergistic effects of pairwise drug combinations from gene microarray data
-
Jin, G., Zhao, H., Zhou, X., Wong, S.T.C. An enhanced Petri-Net model to predict synergistic effects of pairwise drug combinations from gene microarray data. Bioinformatics 2011, 27.
-
(2011)
Bioinformatics
, pp. 27
-
-
Jin, G.1
Zhao, H.2
Zhou, X.3
Wong, S.T.C.4
-
32
-
-
84855381399
-
A novel method of transcriptional response analysis to facilitate drug repositioning for cancer therapy
-
Jin, G., Fu, C., Zhao, H., Cui, K., Chang, J., Wong, S.T.C. A novel method of transcriptional response analysis to facilitate drug repositioning for cancer therapy. Cancer Res. 2012, 72, 33-44.
-
(2012)
Cancer Res
, vol.72
, pp. 33-44
-
-
Jin, G.1
Fu, C.2
Zhao, H.3
Cui, K.4
Chang, J.5
Wong, S.T.C.6
-
33
-
-
84884200376
-
Characterization of drug-induced transcriptional modules: Towards drug repositioning and functional understanding
-
Iskar, M., Zeller, G., Blattmann, P., Campillos, M., Kuhn, M., Kaminska, K.H., Runz, H., Gavin, A.C., Pepperkok, R., Van Noort, V., et al. Characterization of drug-induced transcriptional modules: Towards drug repositioning and functional understanding. Mol. Syst. Biol. 2013, 9.
-
(2013)
Mol. Syst. Biol
, pp. 9
-
-
Iskar, M.1
Zeller, G.2
Blattmann, P.3
Campillos, M.4
Kuhn, M.5
Kaminska, K.H.6
Runz, H.7
Gavin, A.C.8
Pepperkok, R.9
Van Noort, V.10
-
34
-
-
84891634739
-
Beyond modules and hubs: The potential of gene coexpression networks for investigating molecular mechanisms of complex brain disorders
-
Gaiteri, C., Ding, Y., French, B., Tseng, G.C., Sibille, E. Beyond modules and hubs: The potential of gene coexpression networks for investigating molecular mechanisms of complex brain disorders. Genes Brain Behav. 2014,13,13-24.
-
(2014)
Genes Brain Behav
, vol.13
, pp. 13-24
-
-
Gaiteri, C.1
Ding, Y.2
French, B.3
Tseng, G.C.4
Sibille, E.5
-
35
-
-
84875718672
-
Transcriptional data: A new gateway to drug repositioning
-
Iorio, F., Rittman, T., Ge, H., Menden, M., Saez-Rodriguez, J. Transcriptional data: A new gateway to drug repositioning? Drug Discov. Today 2013,18, 350-357.
-
(2013)
Drug Discov. Today
, vol.18
, pp. 350-357
-
-
Iorio, F.1
Rittman, T.2
Ge, H.3
Menden, M.4
Saez-Rodriguez, J.5
-
36
-
-
80053293396
-
Discovery and preclinical validation of drug indications using compendia of public gene expression data (Science Translational Medicine (2011) 3, (102er))
-
Sirota, M., Dudley, J.T., Kim, J., Chiang, A.P., Morgan, A.A., Sweet-Cordero, A., Sage, J., Butte, A.J. Discovery and preclinical validation of drug indications using compendia of public gene expression data (Science Translational Medicine (2011) 3, (102er)). Sci. Transl. Med. 2011, 3, 96ra77.
-
(2011)
Sci. Transl. Med
, vol.3
-
-
Sirota, M.1
Dudley, J.T.2
Kim, J.3
Chiang, A.P.4
Morgan, A.A.5
Sweet-Cordero, A.6
Sage, J.7
Butte, A.J.8
-
37
-
-
85048345276
-
A machine learning approach to drug repositioning based on drug expression profiles: Applications in psychiatry
-
arXiv:1706.03014
-
Zhao, K., So, H.-C. A machine learning approach to drug repositioning based on drug expression profiles: Applications in psychiatry. arXiv 2017, arXiv:1706.03014.
-
(2017)
Arxiv
-
-
Zhao, K.1
So, H.-C.2
-
38
-
-
85032867588
-
Unsupervised gene expression analyses identify IPF-severity correlated signatures, associated genes and biomarkers
-
Wang, Y., Yella, J., Chen, J., McCormack, F.X., Madala, S.K., Jegga, A.G. Unsupervised gene expression analyses identify IPF-severity correlated signatures, associated genes and biomarkers. BMC Pulm. Med. 2017, 17.
-
(2017)
BMC Pulm. Med
, pp. 17
-
-
Wang, Y.1
Yella, J.2
Chen, J.3
Mc Cormack, F.X.4
Madala, S.K.5
Jegga, A.G.6
-
39
-
-
80052576073
-
Gene Expression Signature Analysis Identifies Vorinostat as a Candidate Therapy for Gastric Cancer
-
Claerhout, S., Lim, J.Y., Choi, W., Park, Y.-Y., Kim, K., Kim, S.-B., Lee, J.-S., Mills, G.B., Cho, J.Y. Gene Expression Signature Analysis Identifies Vorinostat as a Candidate Therapy for Gastric Cancer. PLoS ONE 2011, 6, e24662.
-
(2011)
Plos ONE
, vol.6
-
-
Claerhout, S.1
Lim, J.Y.2
Choi, W.3
Park, Y.-Y.4
Kim, K.5
Kim, S.-B.6
Lee, J.-S.7
Mills, G.B.8
Cho, J.Y.9
-
40
-
-
77956575047
-
Evaluation of phenoxybenzamine in the CFA model of pain following gene expression studies and connectivity mapping
-
Chang, M., Smith, S., Thorpe, A., Barratt, M.J., Karim, F. Evaluation of phenoxybenzamine in the CFA model of pain following gene expression studies and connectivity mapping. Mol. Pain 2010, 6.
-
(2010)
Mol. Pain
, pp. 6
-
-
Chang, M.1
Smith, S.2
Thorpe, A.3
Barratt, M.J.4
Karim, F.5
-
41
-
-
84944725194
-
ADReCS: An ontology database for aiding standardization and hierarchical Classification of adverse drug reaction terms
-
Cai, M.C., Xu, Q., Pan, Y.J., Pan, W., Ji, N., Li, Y.B., Liu, H.J.J.K., Ji, Z.L. ADReCS: An ontology database for aiding standardization and hierarchical Classification of adverse drug reaction terms. Nucleic Acids Res. 2015, 43, D907-D913.
-
(2015)
Nucleic Acids Res
, vol.43
-
-
Cai, M.C.1
Xu, Q.2
Pan, Y.J.3
Pan, W.4
Ji, N.5
Li, Y.B.6
Liu, H.J.J.K.7
Ji, Z.L.8
-
42
-
-
84862192766
-
ChEMBL: A large-scale bioactivity database for drug discovery
-
Gaulton, A., Bellis, L.J., Bento, A.P., Chambers, J., Davies, M., Hersey, A., Light, Y., McGlinchey, S., Michalovich, D., Al-Lazikani, B., et al. ChEMBL: A large-scale bioactivity database for drug discovery. Nucleic Acids Res. 2012, 40.
-
(2012)
Nucleic Acids Res.
, pp. 40
-
-
Gaulton, A.1
Bellis, L.J.2
Bento, A.P.3
Chambers, J.4
Davies, M.5
Hersey, A.6
Light, Y.7
Mc Glinchey, S.8
Michalovich, D.9
Al-Lazikani, B.10
-
43
-
-
44649178588
-
Internet-based tools for communication and collaboration in chemistry
-
Williams, A.J. Internet-based tools for communication and collaboration in chemistry. Drug Discov. Today 2008,13, 502-506.
-
(2008)
Drug Discov. Today
, vol.13
, pp. 502-506
-
-
Williams, A.J.1
-
44
-
-
85036572148
-
A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles
-
Subramanian, A., Narayan, R., Corsello, S.M., Peck, D.D., Natoli, T.E., Lu, X., Gould, J., Davis, J.F., Tubelli, A.A., Asiedu, J.K., et al. A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles. Cell 2017,171,1437-1452.
-
(2017)
Cell
, vol.171
, pp. 1437-1452
-
-
Subramanian, A.1
Narayan, R.2
Corsello, S.M.3
Peck, D.D.4
Natoli, T.E.5
Lu, X.6
Gould, J.7
Davis, J.F.8
Tubelli, A.A.9
Asiedu, J.K.10
-
45
-
-
0037501328
-
The Comparative Toxicogenomics Database (CTD)
-
Mattingly, C.J., Colby, G.T., Forrest, J.N., Boyer, J.L. The Comparative Toxicogenomics Database (CTD). Environ. Health Perspect. 2003,111, 793.
-
(2003)
Environ. Health Perspect.
, vol.111
, pp. 793
-
-
Mattingly, C.J.1
Colby, G.T.2
Forrest, J.N.3
Boyer, J.L.4
-
46
-
-
85048321626
-
-
(accessed on 25 April 2018)
-
National Institutes of Health: Health & Human Services DailyMed. Available online: http://dailymed.nlm. nih.gov/dailymed/index.cfm (accessed on 25 April 2018).
-
-
-
-
47
-
-
84888862866
-
DGIdb: Mining the druggable genome
-
Griffith, M., Griffith, O.L., Coffman, A.C., Weible, J.V., Mcmichael, J.F., Spies, N.C., Koval, J., Das, I., Callaway, M.B., Eldred, J.M., et al. DGIdb: Mining the druggable genome. Nat. Methods 2013,10,1209-1210.
-
(2013)
Nat. Methods
, vol.10
, pp. 1209-1210
-
-
Griffith, M.1
Griffith, O.L.2
Coffman, A.C.3
Weible, J.V.4
Mc Michael, J.F.5
Spies, N.C.6
Koval, J.7
Das, I.8
Callaway, M.B.9
Eldred, J.M.10
-
48
-
-
85048313414
-
-
accessed on 22 April
-
DrugBank DrugBank. Available online: http://www.drugbank.ca (accessed on 22 April 2018).
-
(2018)
-
-
-
49
-
-
85016084712
-
DrugCentral: Online drug compendium
-
Ursu, O., Holmes, J., Knockel, J., Bologa, C.G., Yang, J.J., Mathias, S.L., Nelson, S.J., Oprea, T.I. DrugCentral: Online drug compendium. Nucleic Acids Res. 2017, 45, D932-D939.
-
(2017)
Nucleic Acids Res
, vol.45
, pp. D932-D939
-
-
Ursu, O.1
Holmes, J.2
Knockel, J.3
Bologa, C.G.4
Yang, J.J.5
Mathias, S.L.6
Nelson, S.J.7
Oprea, T.I.8
-
50
-
-
84861729758
-
E-Drug3D: 3D structure collections dedicated to drug repurposing and fragment-based drug design
-
Pihan, E., Colliandre, L., Guichou, J.F., Douguet, D. E-Drug3D: 3D structure collections dedicated to drug repurposing and fragment-based drug design. Bioinformatics 2012, 28,1540-1541.
-
(2012)
Bioinformatics
, vol.28
, pp. 1540-1541
-
-
Pihan, E.1
Colliandre, L.2
Guichou, J.F.3
Douguet, D.4
-
51
-
-
84876563391
-
Genomics of Drug Sensitivity in Cancer (GDSC): A resource for therapeutic biomarker discovery in cancer cells
-
Yang, W., Soares, J., Greninger, P., Edelman, E.J., Lightfoot, H., Forbes, S., Bindal, N., Beare, D., Smith, J.A., Thompson, I.R., et al. Genomics of Drug Sensitivity in Cancer (GDSC): A resource for therapeutic biomarker discovery in cancer cells. Nucleic Acids Res. 2013, 41.
-
(2013)
Nucleic Acids Res.
, pp. 41
-
-
Yang, W.1
Soares, J.2
Greninger, P.3
Edelman, E.J.4
Lightfoot, H.5
Forbes, S.6
Bindal, N.7
Beare, D.8
Smith, J.A.9
Thompson, I.R.10
-
52
-
-
85016064721
-
Open Targets: A platform for therapeutic target identification and Validation
-
Koscielny, G., An, P., Carvalho-Silva, D., Cham, J.A., Fumis, L., Gasparyan, R., Hasan, S., Karamanis, N., Maguire, M., Papa, E., et al. Open Targets: A platform for therapeutic target identification and Validation. Nucleic Acids Res. 2017, 45, D985-D994.
-
(2017)
Nucleic Acids Res
, vol.45
-
-
Koscielny, G.1
An, P.2
Carvalho-Silva, D.3
Cham, J.A.4
Fumis, L.5
Gasparyan, R.6
Hasan, S.7
Karamanis, N.8
Maguire, M.9
Papa, E.10
-
53
-
-
0036088113
-
PharmGKB: The pharmacogenetics knowledge base
-
Hewett, M., Oliver, D.E., Rubin, D.L., Easton, K.L., Stuart, J.M., Altman, R.B., Klein, T.E. PharmGKB: The pharmacogenetics knowledge base. Nucleic Acids Res. 2002, 30,163-165.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 163-165
-
-
Hewett, M.1
Oliver, D.E.2
Rubin, D.L.3
Easton, K.L.4
Stuart, J.M.5
Altman, R.B.6
Klein, T.E.7
-
54
-
-
84929377653
-
PkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures
-
Pires, D.E.V., Blundell, T.L., Ascher, D.B. pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. J. Med. Chem. 2015, 58, 4066-4072.
-
(2015)
J. Med. Chem.
, vol.58
, pp. 4066-4072
-
-
Pires, D.E.V.1
Blundell, T.L.2
Ascher, D.B.3
-
55
-
-
84925867952
-
Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies
-
Cowley, G.S., Weir, B.A., Vazquez, F., Tamayo, P., Scott, J.A., Rusin, S., East-Seletsky, A., Ali, L.D., Gerath, W.F.J., Pantel, S.E., et al. Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies. Sci. Data 2014,1.
-
(2014)
Sci. Data
, pp. 1
-
-
Cowley, G.S.1
Weir, B.A.2
Vazquez, F.3
Tamayo, P.4
Scott, J.A.5
Rusin, S.6
East-Seletsky, A.7
Ali, L.D.8
Gerath, W.F.J.9
Pantel, S.E.10
-
56
-
-
78651321625
-
PROMISCUOUS: A database for network-based drug-repositioning
-
Von Eichborn, J., Murgueitio, M.S., Dunkel, M., Koerner, S., Bourne, P.E., Preissner, R. PROMISCUOUS: A database for network-based drug-repositioning. Nucleic Acids Res. 2011, 39.
-
(2011)
Nucleic Acids Res.
, pp. 39
-
-
Von Eichborn, J.1
Murgueitio, M.S.2
Dunkel, M.3
Koerner, S.4
Bourne, P.E.5
Preissner, R.6
-
57
-
-
84979586933
-
PubChem substance and compound databases
-
Kim, S., Thiessen, P.A., Bolton, E.E., Chen, J., Fu, G., Gindulyte, A., Han, L., He, J., He, S., Shoemaker, B.A., et al. PubChem substance and compound databases. Nucleic Acids Res. 2016, 44, D1202-D1213.
-
(2016)
Nucleic Acids Res
, vol.44
-
-
Kim, S.1
Thiessen, P.A.2
Bolton, E.E.3
Chen, J.4
Fu, G.5
Gindulyte, A.6
Han, L.7
He, J.8
He, S.9
Shoemaker, B.A.10
-
58
-
-
84979503522
-
The SIDER database of drugs and side effects
-
Kuhn, M., Letunic, I., Jensen, L.J., Bork, P. The SIDER database of drugs and side effects. Nucleic Acids Res. 2016, 44, D1075-D1079.
-
(2016)
Nucleic Acids Res
, vol.44
-
-
Kuhn, M.1
Letunic, I.2
Jensen, L.J.3
Bork, P.4
-
59
-
-
38549130733
-
Interaction networks of chemicals and proteins
-
Kuhn, M., von Mering, C., Campillos, M., Jensen, L.J., Bork, P. STITCH: Interaction networks of chemicals and proteins. Nucleic Acids Res. 2008, 36.
-
(2008)
Nucleic Acids Res
, pp. 36
-
-
Kuhn, M.1
Von Mering, C.2
Campillos, M.3
Jensen, L.J.4
Bork, P.5
-
60
-
-
48449090136
-
SuperPred: Drug classification and target prediction
-
Dunkel, M., Günther, S., Ahmed, J., Wittig, B., Preissner, R. SuperPred: Drug classification and target prediction. Nucleic Acids Res. 2008, 36.
-
(2008)
Nucleic Acids Res
, pp. 36
-
-
Dunkel, M.1
Günther, S.2
Ahmed, J.3
Wittig, B.4
Preissner, R.5
-
61
-
-
0036084258
-
Therapeutic Target Database
-
Chen, X., Ji, Z.L., Chen, Y.Z. TTD: Therapeutic Target Database. Nucleic Acids Res. 2002, 30, 412-415.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 412-415
-
-
Chen, X.1
Ji, Z.L.2
Chen, Y.3
-
62
-
-
84946074829
-
T3DB: The toxic exposome database
-
Wishart, D., Arndt, D., Pon, A., Sajed, T., Guo, A.C., Djoumbou, Y., Knox, C., Wilson, M., Liang, Y., Grant, J., et al. T3DB: The toxic exposome database. Nucleic Acids Res. 2015, 43, D928-D934.
-
(2015)
Nucleic Acids Res
, vol.43
-
-
Wishart, D.1
Arndt, D.2
Pon, A.3
Sajed, T.4
Guo, A.C.5
Djoumbou, Y.6
Knox, C.7
Wilson, M.8
Liang, Y.9
Grant, J.10
-
63
-
-
84920269464
-
Proteomics. Tissue-based map of the human proteome
-
Uhlén, M., Fagerberg, L., Hallstrom, B.M., Lindskog, C., Oksvold, P., Mardinoglu, A., Sivertsson, À., Kampf, C., Sjostedt, E., Asplund, A., et al. Proteomics. Tissue-based map of the human proteome. Science 2015, 347,1260419.
-
(2015)
Science
, vol.347
, pp. 1260419
-
-
Uhlén, M.1
Fagerberg, L.2
Hallstrom, B.M.3
Lindskog, C.4
Oksvold, P.5
Mardinoglu, A.6
Sivertsson, À.7
Kampf, C.8
Sjostedt, E.9
Asplund, A.10
-
64
-
-
0032919364
-
Kyoto encyclopedia of genes and genomes
-
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., Kanehisa, M. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 1999,27,29-34.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 29-34
-
-
Ogata, H.1
Goto, S.2
Sato, K.3
Fujibuchi, W.4
Bono, H.5
Kanehisa, M.6
-
65
-
-
84948741313
-
The PsychENCODE project
-
Akbarian, S., Liu, C., Knowles, J.A., Vaccarino, F.M., Farnham, P.J., Crawford, G.E., Jaffe, A.E., Pinto, D., Dracheva, S., Geschwind, D.H., et al. The PsychENCODE project. Nat. Neurosci. 2015, 18, 1707-1712.
-
(2015)
Nat. Neurosci.
, vol.18
, pp. 1707-1712
-
-
Akbarian, S.1
Liu, C.2
Knowles, J.A.3
Vaccarino, F.M.4
Farnham, P.J.5
Crawford, G.E.6
Jaffe, A.E.7
Pinto, D.8
Dracheva, S.9
Geschwind, D.H.10
-
66
-
-
84876555679
-
Allen Brain Atlas: An integrated spatio-temporal portal for exploring the central nervous system
-
Sunkin, S.M., Ng, L., Lau, C., Dolbeare, T., Gilbert, T.L., Thompson, C.L., Hawrylycz, M., Dang, C. Allen Brain Atlas: An integrated spatio-temporal portal for exploring the central nervous system. Nucleic Acids Res. 2013, 41, D996-D1008.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. DD996-D1008
-
-
Sunkin, S.M.1
Ng, L.2
Lau, C.3
Dolbeare, T.4
Gilbert, T.L.5
Thompson, C.L.6
Hawrylycz, M.7
Dang, C.8
-
67
-
-
13444249955
-
ArrayExpress-a public repository for microarray gene expression data at the EBI
-
Parkinson, H. ArrayExpress-a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 2004, 33, D553-D555.
-
(2004)
Nucleic Acids Res
, vol.33
, pp. D553-D555
-
-
Parkinson, H.1
-
68
-
-
84859169877
-
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity Supp
-
Barretina, J., Caponigro, G., Stransky, N., Venkatesan, K., Margolin, A.A; Kim, S., Wilson, C.J., Lehar, J., Kryukov, G.V; Sonkin, D., et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity Supp. Nature 2012, 483, 603-607.
-
(2012)
Nature
, vol.483
, pp. 603-607
-
-
Barretina, J.1
Caponigro, G.2
Stransky, N.3
Venkatesan, K.4
Margolin, A.A.5
Kim, S.6
Wilson, C.J.7
Lehar, J.8
Kryukov, G.V.9
Sonkin, D.10
-
69
-
-
84946040120
-
COSMIC: Exploring the world's knowledge of somatic mutations in human cancer
-
Forbes, S.A., Beare, D., Gunasekaran, P., Leung, K., Bindal, N., Boutselakis, H., Ding, M., Bamford, S., Cole, C., Ward, S., et al. COSMIC: Exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res. 2015, 43, D805-D811.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. D805-D811
-
-
Forbes, S.A.1
Beare, D.2
Gunasekaran, P.3
Leung, K.4
Bindal, N.5
Boutselakis, H.6
Ding, M.7
Bamford, S.8
Cole, C.9
Ward, S.10
-
70
-
-
34748848639
-
The NCBI dbGaP database of genotypes and phenotypes
-
Mailman, M.D., Feolo, M., Jin, Y., Kimura, M., Tryka, K., Bagoutdinov, R., Hao, L., Kiang, A., Paschall, J., Phan, L., et al. The NCBI dbGaP database of genotypes and phenotypes. Nat. Genet. 2007, 39,1181-1186.
-
(2007)
Nat. Genet.
, vol.39
, pp. 1181-1186
-
-
Mailman, M.D.1
Feolo, M.2
Jin, Y.3
Kimura, M.4
Tryka, K.5
Bagoutdinov, R.6
Hao, L.7
Kiang, A.8
Paschall, J.9
Phan, L.10
-
71
-
-
0035173378
-
DbSNP: The NCBI database of genetic variation
-
Sherry, S.T. dbSNP: The NCBI database of genetic variation. Nucleic Acids Res. 2001, 29, 308-311.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 308-311
-
-
Sherry, S.T.1
-
72
-
-
84876527890
-
DbVar and DGVa: Public archives for genomic structural variation
-
Lappalainen, I., Lopez, J., Skipper, L., Hefferon, T., Spalding, J.D., Garner, J., Chen, C., Maguire, M., Corbett, M., Zhou, G., et al. DbVar and DGVa: Public archives for genomic structural variation. Nucleic Acids Res. 2013, 41.
-
(2013)
Nucleic Acids Res
, pp. 41
-
-
Lappalainen, I.1
Lopez, J.2
Skipper, L.3
Hefferon, T.4
Spalding, J.D.5
Garner, J.6
Chen, C.7
Maguire, M.8
Corbett, M.9
Zhou, G.10
-
73
-
-
84939221315
-
DisGeNET: A discovery platform for the dynamical exploration of human diseases and their genes
-
Pinero, J., Queralt-Rosinach, N., Bravo, À., Deu-Pons, J., Bauer-Mehren, A., Baron, M., Sanz, F., Furlong, L.I. DisGeNET: A discovery platform for the dynamical exploration of human diseases and their genes. Database 2015, 2015.
-
(2015)
Database
, pp. 2015
-
-
Pinero, J.1
Queralt-Rosinach, N.2
Bravo, À.3
Deu-Pons, J.4
Bauer-Mehren, A.5
Baron, M.6
Sanz, F.7
Furlong, L.I.8
-
74
-
-
84988850450
-
Toward a Shared Vision for Cancer Genomic Data
-
Grossman, R.L., Heath, A.P., Ferretti, V., Varmus, H.E., Lowy, D.R., Kibbe, W.A., Staudt, L.M. Toward a Shared Vision for Cancer Genomic Data. N. Engl. J. Med. 2016, 375,1109-1112.
-
(2016)
N. Engl. J. Med.
, vol.375
, pp. 1109-1112
-
-
Grossman, R.L.1
Heath, A.P.2
Ferretti, V.3
Varmus, H.E.4
Lowy, D.R.5
Kibbe, W.A.6
Staudt, L.M.7
-
75
-
-
13444304325
-
NCBI GEO: Mining millions of expression profiles-database and tools
-
Barrett, T. NCBI GEO: Mining millions of expression profiles-database and tools. Nucleic Acids Res. 2004, 33, D562-D566.
-
(2004)
Nucleic Acids Res
, vol.33
-
-
Barrett, T.1
-
76
-
-
84878682420
-
The Genotype-Tissue Expression (GTEx) project
-
Lonsdale, J., Thomas, J., Salvatore, M., Phillips, R., Lo, E., Shad, S., Hasz, R., Walters, G., Garcia, F., Young, N., et al. The Genotype-Tissue Expression (GTEx) project. Nat. Genet. 2013, 45, 580-585.
-
(2013)
Nat. Genet.
, vol.45
, pp. 580-585
-
-
Lonsdale, J.1
Thomas, J.2
Salvatore, M.3
Phillips, R.4
Lo, E.5
Shad, S.6
Hasz, R.7
Walters, G.8
Garcia, F.9
Young, N.10
-
77
-
-
84901599553
-
A draft map of the human proteome
-
Kim, M.-S., Pinto, S.M., Getnet, D., Nirujogi, R.S., Manda, S.S., Chaerkady, R., Madugundu, A.K., Kelkar, D.S., Isserlin, R., Jain, S., et al. A draft map of the human proteome. Nature 2014, 509, 575-581.
-
(2014)
Nature
, vol.509
, pp. 575-581
-
-
Kim, M.-S.1
Pinto, S.M.2
Getnet, D.3
Nirujogi, R.S.4
Manda, S.S.5
Chaerkady, R.6
Madugundu, A.K.7
Kelkar, D.S.8
Isserlin, R.9
Jain, S.10
-
78
-
-
84969928691
-
International Cancer Genome Consortium
-
Cancer, T. International Cancer Genome Consortium. Cancer 2011, 2011,1-20.
-
(2011)
Cancer
, vol.2011
, pp. 1-20
-
-
Cancer, T.1
-
79
-
-
85016146534
-
The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data
-
Clarke, L., Fairley, S., Zheng-Bradley, X., Streeter, I., Perry, E., Lowy, E., Tassé, A.M., Flicek, P. The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data. Nucleic Acids Res. 2017, 45, D854-D859.
-
(2017)
Nucleic Acids Res
, vol.45
, pp. D854-D859
-
-
Clarke, L.1
Fairley, S.2
Zheng-Bradley, X.3
Streeter, I.4
Perry, E.5
Lowy, E.6
Tassé, A.M.7
Flicek, P.8
-
81
-
-
77957940722
-
The NIH roadmap epigenomics mapping consortium
-
Bernstein, B.E., Stamatoyannopoulos, J.A., Costello, J.F., Ren, B., Milosavljevic, A., Meissner, A., Kellis, M., Marra, M.A., Beaudet, A.L., Ecker, J.R., et al. The NIH roadmap epigenomics mapping consortium. Nat. Biotechnol. 2010, 28,1045-1048.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 1045-1048
-
-
Bernstein, B.E.1
Stamatoyannopoulos, J.A.2
Costello, J.F.3
Ren, B.4
Milosavljevic, A.5
Meissner, A.6
Kellis, M.7
Marra, M.A.8
Beaudet, A.L.9
Ecker, J.R.10
-
82
-
-
78651324347
-
The STRING database in 2011: Functional interaction networks of proteins, globally integrated and scored
-
Szklarczyk, D., Franceschini, A., Kuhn, M., Simonovic, M., Roth, A., Minguez, P., Doerks, T., Stark, M., Muller, J., Bork, P., et al. The STRING database in 2011: Functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 2011, 39.
-
(2011)
Nucleic Acids Res
, pp. 39
-
-
Szklarczyk, D.1
Franceschini, A.2
Kuhn, M.3
Simonovic, M.4
Roth, A.5
Minguez, P.6
Doerks, T.7
Stark, M.8
Muller, J.9
Bork, P.10
-
83
-
-
33749335282
-
The connectivity map: Using gene-expression signatures to connect small molecules, genes, and disease
-
Lamb, J., Crawford, E.D., Peck, D., Modell, J.W., Blat, I.C., Wrobel, M.J., Lerner, J., Brunet, J.P., Subramanian, A., Ross, K.N., et al. The connectivity map: Using gene-expression signatures to connect small molecules, genes, and disease. Science 2006, 313,1929-1935.
-
(2006)
Science
, vol.313
, pp. 1929-1935
-
-
Lamb, J.1
Crawford, E.D.2
Peck, D.3
Modell, J.W.4
Blat, I.C.5
Wrobel, M.J.6
Lerner, J.7
Brunet, J.P.8
Subramanian, A.9
Ross, K.N.10
-
84
-
-
85029518999
-
A review of connectivity map and computational approaches in pharmacogenomics
-
Musa, A., Ghoraie, L.S., Zhang, S.-D., Galzko, G., Yli-Harja, O., Dehmer, M., Haibe-Kains, B., Emmert-Streib, F. A review of connectivity map and computational approaches in pharmacogenomics. Brief. Bioinform. 2017, bbw112.
-
(2017)
Brief. Bioinform
-
-
Musa, A.1
Ghoraie, L.S.2
Zhang, S.-D.3
Galzko, G.4
Yli-Harja, O.5
Dehmer, M.6
Haibe-Kains, B.7
Emmert-Streib, F.8
-
85
-
-
84980022857
-
Deep Learning for Computational Biology
-
Angermueller, C., Parnamaa, T., Parts, L., Oliver, S. Deep Learning for Computational Biology. Mol. Syst. Biol. 2016, 878.
-
(2016)
Mol. Syst. Biol.
, pp. 878
-
-
Angermueller, C.1
Parnamaa, T.2
Parts, L.3
Oliver, S.4
-
86
-
-
79958754253
-
PREDICT: A method for inferring novel drug indications with application to personalized medicine
-
Gottlieb, A., Stein, G.Y., Ruppin, E., Sharan, R. PREDICT: A method for inferring novel drug indications with application to personalized medicine. Mol. Syst. Biol. 2011, 7.
-
(2011)
Mol. Syst. Biol.
, pp. 7
-
-
Gottlieb, A.1
Stein, G.Y.2
Ruppin, E.3
Sharan, R.4
-
87
-
-
84941649312
-
Similarity-based prediction for Anatomical Therapeutic Chemical classification of drugs by integrating multiple data sources
-
Liu, Z., Guo, F., Gu, J., Wang, Y., Li, Y., Wang, D., Lu, L., Li, D., He, F. Similarity-based prediction for Anatomical Therapeutic Chemical classification of drugs by integrating multiple data sources. Bioinformatics 2015, 31, 1788-1795.
-
(2015)
Bioinformatics
, vol.31
, pp. 1788-1795
-
-
Liu, Z.1
Guo, F.2
Gu, J.3
Wang, Y.4
Li, Y.5
Wang, D.6
Lu, L.7
Li, D.8
He, F.9
-
88
-
-
84872558849
-
A new method for computational drug repositioning using drug pairwise similarity
-
Philadelphia, PA, USA, 4-7 October
-
Li, J., Lu, Z. A new method for computational drug repositioning using drug pairwise similarity. In Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2012, Philadelphia, PA, USA, 4-7 October 2012; pp. 453-456.
-
(2012)
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2012
, pp. 453-456
-
-
Li, J.1
Lu, Z.2
-
89
-
-
84990913647
-
Drug repositioning based on comprehensive similarity measures and Bi-Random walk algorithm
-
Luo, H., Wang, J., Li, M., Luo, J., Peng, X., Wu, F.X., Pan, Y. Drug repositioning based on comprehensive similarity measures and Bi-Random walk algorithm. Bioinformatics 2016, 32,2664-2671.
-
(2016)
Bioinformatics
, vol.32
, pp. 2664-2671
-
-
Luo, H.1
Wang, J.2
Li, M.3
Luo, J.4
Peng, X.5
Wu, F.X.6
Pan, Y.7
-
90
-
-
84909606201
-
A network-based classification model for deriving novel drug-disease associations and assessing their molecular actions
-
Oh, M., Ahn, J., Yoon, Y. A network-based classification model for deriving novel drug-disease associations and assessing their molecular actions. PLoS ONE 2014, 9.
-
(2014)
Plos ONE
, pp. 9
-
-
Oh, M.1
Ahn, J.2
Yoon, Y.3
-
91
-
-
84968861400
-
Applications of Deep Learning in Biomedicine
-
Mamoshina, P., Vieira, A., Putin, E., Zhavoronkov, A. Applications of Deep Learning in Biomedicine. Mol. Pharm. 2016,13,1445-1454.
-
(2016)
Mol. Pharm.
, vol.13
, pp. 1445-1454
-
-
Mamoshina, P.1
Vieira, A.2
Putin, E.3
Zhavoronkov, A.4
-
92
-
-
84930630277
-
Deep learning
-
Lecun, Y., Bengio, Y., Hinton, G. Deep learning. Nature 2015, 521, 436-444.
-
(2015)
Nature
, vol.521
, pp. 436-444
-
-
Lecun, Y.1
Bengio, Y.2
Hinton, G.3
-
93
-
-
84979019529
-
Deep learning applications for predicting pharmacological properties of drugs and drug repurposing using transcriptomic data
-
Aliper, A., Plis, S., Artemov, A., Ulloa, A., Mamoshina, P., Zhavoronkov, A. Deep learning applications for predicting pharmacological properties of drugs and drug repurposing using transcriptomic data. Mol. Pharm. 2016,13, 2524-2530.
-
(2016)
Mol. Pharm.
, vol.13
, pp. 2524-2530
-
-
Aliper, A.1
Plis, S.2
Artemov, A.3
Ulloa, A.4
Mamoshina, P.5
Zhavoronkov, A.6
-
94
-
-
85048350085
-
Toxicity Prediction using Deep Learning
-
Unterthiner, T., Mayr, A., Klambauer, G., Hochreiter, S. Toxicity Prediction using Deep Learning. Front. Environ. Sci. 2015, 3,10.
-
(2015)
Front. Environ. Sci.
, vol.3
, pp. 10
-
-
Unterthiner, T.1
Mayr, A.2
Klambauer, G.3
Hochreiter, S.4
-
95
-
-
84927735077
-
Massively Multitask Networks for Drug Discovery
-
arXiv:1502.02072
-
Ramsundar, B., Kearnes, S., Riley, P., Webster, D., Konerding, D., Pande, V. Massively Multitask Networks for Drug Discovery. arXiv 2015, arXiv:1502.02072.
-
(2015)
Arxiv
-
-
Ramsundar, B.1
Kearnes, S.2
Riley, P.3
Webster, D.4
Konerding, D.5
Pande, V.6
-
96
-
-
70249134919
-
Molecular networks as sensors and drivers of common human diseases
-
Schadt, E.E. Molecular networks as sensors and drivers of common human diseases. Nature 2009, 461, 218-223.
-
(2009)
Nature
, vol.461
, pp. 218-223
-
-
Schadt, E.E.1
-
97
-
-
84874683213
-
Drug interaction networks: An introduction to translational and clinical applications
-
Azuaje, F. Drug interaction networks: An introduction to translational and clinical applications. Cardiovasc. Res. 2013, 97, 631-641.
-
(2013)
Cardiovasc. Res.
, vol.97
, pp. 631-641
-
-
Azuaje, F.1
-
98
-
-
84895194983
-
Construction of drug network based on side effects and its application for drug repositioning
-
Ye, H., Liu, Q., Wei, J. Construction of drug network based on side effects and its application for drug repositioning. PLoS ONE 2014, 9.
-
(2014)
Plos ONE
, pp. 9
-
-
Ye, H.1
Liu, Q.2
Wei, J.3
-
99
-
-
84866460840
-
Relating drug-protein interaction network with drug side effects
-
Mizutani, S., Pauwels, E., Stoven, V., Goto, S., Yamanishi, Y. Relating drug-protein interaction network with drug side effects. Bioinformatics 2012,28.
-
(2012)
Bioinformatics
, pp. 28
-
-
Mizutani, S.1
Pauwels, E.2
Stoven, V.3
Goto, S.4
Yamanishi, Y.5
-
100
-
-
47249146126
-
Drug target identification using side-effect similarity
-
Campillos, M., Kuhn, M., Gavin, A.-C., Jensen, L.J., Bork, P. Drug target identification using side-effect similarity. Science 2008, 321, 263-266.
-
(2008)
Science
, vol.321
, pp. 263-266
-
-
Campillos, M.1
Kuhn, M.2
Gavin, A.-C.3
Jensen, L.J.4
Bork, P.5
-
101
-
-
84960107641
-
KsRepo: A generalized platform for computational drug repositioning
-
Brown, A.S., Kong, S.W., Kohane, I.S., Patel, C.J. ksRepo: A generalized platform for computational drug repositioning. BMC Bioinform. 2016,17.
-
(2016)
BMC Bioinform
, pp. 17
-
-
Brown, A.S.1
Kong, S.W.2
Kohane, I.S.3
Patel, C.J.4
-
102
-
-
84979864693
-
NFFinder: An online bioinformatics tool for searching similar transcriptomics experiments in the context of drug repositioning
-
Setoain, J., Franch, M., Martinez, M., Tabas-Madrid, D., Sorzano, C.O.S., Bakker, A., Gonzalez-Couto, E., Elvira, J., Pascual-Montano, A. NFFinder: An online bioinformatics tool for searching similar transcriptomics experiments in the context of drug repositioning. Nucleic Acids Res. 2015, 43, W193-W199.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. W193-W199
-
-
Setoain, J.1
Franch, M.2
Martinez, M.3
Tabas-Madrid, D.4
Sorzano, C.O.S.5
Bakker, A.6
Gonzalez-Couto, E.7
Elvira, J.8
Pascual-Montano, A.9
-
103
-
-
79960897495
-
A novel knowledge-driven systems biology approach for phenotype prediction upon genetic intervention
-
Chang, R., Shoemaker, R., Wang, W. A novel knowledge-driven systems biology approach for phenotype prediction upon genetic intervention. IEEE/ACM Trans. Comput. Biol. Bioinform. 2011, 8, 1170-1182.
-
(2011)
IEEE/ACM Trans. Comput. Biol. Bioinform.
, vol.8
, pp. 1170-1182
-
-
Chang, R.1
Shoemaker, R.2
Wang, W.3
-
104
-
-
84928753287
-
Network-based inference methods for drug repositioning
-
Chen, H., Zhang, H., Zhang, Z., Cao, Y., Tang, W. Network-based inference methods for drug repositioning. Comput. Math. Methods Med. 2015,2015.
-
(2015)
Comput. Math. Methods Med.
, pp. 2015
-
-
Chen, H.1
Zhang, H.2
Zhang, Z.3
Cao, Y.4
Tang, W.5
-
105
-
-
84889655691
-
Computational drug repositioning through heterogeneous network clustering
-
Wu, C., Gudivada, R.C., Aronow, B.J., Jegga, A.G. Computational drug repositioning through heterogeneous network clustering. BMC Syst. Biol. 2013, 7,1-9.
-
(2013)
BMC Syst. Biol.
, vol.7
, pp. 1-9
-
-
Wu, C.1
Gudivada, R.C.2
Aronow, B.J.3
Jegga, A.G.4
-
106
-
-
67849130563
-
ToppGene Suite for gene list enrichment analysis and candidate gene prioritization
-
Chen, J., Bardes, E.E., Aronow, B.J., Jegga, A.G. ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res. 2009, 37.
-
(2009)
Nucleic Acids Res.
, pp. 37
-
-
Chen, J.1
Bardes, E.E.2
Aronow, B.J.3
Jegga, A.G.4
-
107
-
-
85029583555
-
A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information
-
Luo, Y., Zhao, X., Zhou, J., Yang, J., Zhang, Y., Kuang, W., Peng, J., Chen, L., Zeng, J. A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information. Nat. Commun.2017, 8.
-
(2017)
Nat. Commun
, pp. 8
-
-
Luo, Y.1
Zhao, X.2
Zhou, J.3
Yang, J.4
Zhang, Y.5
Kuang, W.6
Peng, J.7
Chen, L.8
Zeng, J.9
-
108
-
-
85032925956
-
Systematic integration of biomedical knowledge prioritizes drugs for repurposing
-
Himmelstein, D.S., Lizee, A., Hessler, C., Brueggeman, L., Chen, S.L., Hadley, D., Green, A., Khankhanian, P., Baranzini, S.E. Systematic integration of biomedical knowledge prioritizes drugs for repurposing. eLife 2017, 6.1-35.
-
(2017)
Elife
, vol.6
, pp. 1-35
-
-
Himmelstein, D.S.1
Lizee, A.2
Hessler, C.3
Brueggeman, L.4
Chen, S.L.5
Hadley, D.6
Green, A.7
Khankhanian, P.8
Baranzini, S.E.9
-
109
-
-
85021117594
-
Natural Language Processing for EHR-Based Pharmacovigilance: A Structured Review
-
Luo, Y., Thompson, W.K., Herr, T.M., Zeng, Z., Berendsen, M.A., Jonnalagadda, S.R., Carson, M.B., Starren, J. Natural Language Processing for EHR-Based Pharmacovigilance: A Structured Review. Drug Saf. 2017, 40, 1075-1089.
-
(2017)
Drug Saf
, vol.40
, pp. 1075-1089
-
-
Luo, Y.1
Thompson, W.K.2
Herr, T.M.3
Zeng, Z.4
Berendsen, M.A.5
Jonnalagadda, S.R.6
Carson, M.B.7
Starren, J.8
-
110
-
-
85027911145
-
Validating drug repurposing signals using electronic health records: A case study of metformin associated with reduced cancer mortality
-
Xu, H., Aldrich, M.C., Chen, Q., Liu, H., Peterson, N.B., Dai, Q., Levy, M., Shah, A., Han, X., Ruan, X., et al. Validating drug repurposing signals using electronic health records: A case study of metformin associated with reduced cancer mortality. J. Am. Med. Inform. Assoc. 2014,1-10.
-
(2014)
J. Am. Med. Inform. Assoc.
, pp. 1-10
-
-
Xu, H.1
Aldrich, M.C.2
Chen, Q.3
Liu, H.4
Peterson, N.B.5
Dai, Q.6
Levy, M.7
Shah, A.8
Han, X.9
Ruan, X.10
-
111
-
-
85041192028
-
A review of validation strategies for computational drug repositioning
-
Brown, A.S., Patel, C.J. A review of validation strategies for computational drug repositioning. Brief. Bioinform. 2018,19,174-177.
-
(2018)
Brief. Bioinform.
, vol.19
, pp. 174-177
-
-
Brown, A.S.1
Patel, C.J.2
-
112
-
-
85016650523
-
Open access target validation is a more efficient way to accelerate drug discovery
-
Lee, W.H. Open access target validation is a more efficient way to accelerate drug discovery. PLoS Biol. 2015, 13.1-9.
-
(2015)
Plos Biol
, vol.13
, pp. 1-9
-
-
Lee, W.H.1
-
113
-
-
85014509390
-
Establishing a reliable framework for harnessing the creative power of the scientific crowd
-
Carter, A.J., Donner, A., Lee, W.H., Bountra, C. Establishing a reliable framework for harnessing the creative power of the scientific crowd. PLoS Biol. 2017,15.
-
(2017)
Plos Biol.
, pp. 15
-
-
Carter, A.J.1
Donner, A.2
Lee, W.H.3
Bountra, C.4
-
114
-
-
84976579967
-
The European lead factory-An experiment in colla-borative drug discovery
-
Rijnders, T.W., Tzalis, D., Jaroch, S. The European lead factory-An experiment in colla-borative drug discovery. J. Med. Dev. Sci. 2015,1, 20-33.
-
(2015)
J. Med. Dev. Sci.
, vol.1
, pp. 20-33
-
-
Rijnders, T.W.1
Tzalis, D.2
Jaroch, S.3
-
115
-
-
77951427922
-
Can open-source drug RD repower pharmaceutical innovation?
-
Munos, B. Can open-source drug RD repower pharmaceutical innovation? Clin. Pharmacol. Ther. 2010, 87, 534-536.
-
(2010)
Clin. Pharmacol. Ther.
, vol.87
, pp. 534-536
-
-
Munos, B.1
-
116
-
-
84873598227
-
Prize-based contests can provide solutions to computational biology problems
-
Lakhani, K.R., Boudreau, K.J., Loh, P.R., Backstrom, L., Baldwin, C., Lonstein, E., Lydon, M., MacCormack, A., Arnaout, R.A., Guinan, E.C. Prize-based contests can provide solutions to computational biology problems. Nat. Biotechnol. 2013, 31,108-111.
-
(2013)
Nat. Biotechnol.
, vol.31
, pp. 108-111
-
-
Lakhani, K.R.1
Boudreau, K.J.2
Loh, P.R.3
Backstrom, L.4
Baldwin, C.5
Lonstein, E.6
Lydon, M.7
Maccormack, A.8
Arnaout, R.A.9
Guinan, E.C.10
-
117
-
-
84876920284
-
Crowd computing: Using competitive dynamics to develop and refine highly predictive models
-
Bentzien, J., Muegge, I., Hamner, B., Thompson, D.C. Crowd computing: Using competitive dynamics to develop and refine highly predictive models. Drug Discov. Today 2013,18, 472-478.
-
(2013)
Drug Discov. Today
, vol.18
, pp. 472-478
-
-
Bentzien, J.1
Muegge, I.2
Hamner, B.3
Thompson, D.C.4
-
118
-
-
84883195998
-
Building a new biomedical ecosystem: Pfizer's centers for therapeutic innovation
-
Patel, A.C., Coyle, A.J. Building a new biomedical ecosystem: Pfizer's centers for therapeutic innovation. Clin. Pharmacol. Ther. 2013, 94, 314-316.
-
(2013)
Clin. Pharmacol. Ther.
, vol.94
, pp. 314-316
-
-
Patel, A.C.1
Coyle, A.J.2
-
119
-
-
84989257090
-
Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd
-
Wang, Z., Monteiro, C.D., Jagodnik, K.M., Fernandez, N.F., Gundersen, G.W., Rouillard, A.D., Jenkins, S.L., Feldmann, A.S., Hu, K.S., McDermott, M.G., et al. Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd. Nat. Commun. 2016, 7.
-
(2016)
Nat. Commun.
, pp. 7
-
-
Wang, Z.1
Monteiro, C.D.2
Jagodnik, K.M.3
Fernandez, N.F.4
Gundersen, G.W.5
Rouillard, A.D.6
Jenkins, S.L.7
Feldmann, A.S.8
Hu, K.S.9
Mc Dermott, M.G.10
-
120
-
-
84925285697
-
Grants4Targets: An open innovation initiative to foster drug discovery collaborations
-
Dorsch, H., Jurock, A.E., Schoepe, S., Lessl, M., Asadullah, K. Grants4Targets: An open innovation initiative to foster drug discovery collaborations. Nat. Rev. Drug Discov. 2014,14, 74.
-
(2014)
Nat. Rev. Drug Discov.
, vol.14
, pp. 74
-
-
Dorsch, H.1
Jurock, A.E.2
Schoepe, S.3
Lessl, M.4
Asadullah, K.5
-
121
-
-
84903700854
-
Scientists see advances in deep learning
-
Markoff, J. Scientists see advances in deep learning. New York Times 2012.
-
(2012)
New York Times
-
-
Markoff, J.1
-
122
-
-
84894094150
-
Open Innovation Drug Discovery (OIDD): A Potential Path to Novel Therapeutic Chemical Space
-
Alvim-Gaston, M., Grese, T., Mahoui, A., Palkowitz, A., Pineiro-Nunez, M., Watson, I. Open Innovation Drug Discovery (OIDD): A Potential Path to Novel Therapeutic Chemical Space. Curr. Top. Med. Chem. 2014, 14, 294-303.
-
(2014)
Curr. Top. Med. Chem.
, vol.14
, pp. 294-303
-
-
Alvim-Gaston, M.1
Grese, T.2
Mahoui, A.3
Palkowitz, A.4
Pineiro-Nunez, M.5
Watson, I.6
-
123
-
-
84877765675
-
Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer
-
Margolin, A.A., Bilal, E., Huang, E., Norman, T.C., Ottestad, L., Mecham, B.H., Sauerwine, B., Kellen, M.R., Mangravite, L.M., Furia, M.D., et al. Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer. Sci. Transl. Med. 2013, 5.
-
(2013)
Sci. Transl. Med.
, pp. 5
-
-
Margolin, A.A.1
Bilal, E.2
Huang, E.3
Norman, T.C.4
Ottestad, L.5
Mecham, B.H.6
Sauerwine, B.7
Kellen, M.R.8
Mangravite, L.M.9
Furia, M.D.10
-
124
-
-
78650385795
-
A Comprehensive Review and Synthesis of Open Source Research
-
Aksulu, A., Wade, M. A Comprehensive Review and Synthesis of Open Source Research. J. Assoc. Inf. Syst. 2010, 11, 576-656.
-
(2010)
J. Assoc. Inf. Syst.
, vol.11
, pp. 576-656
-
-
Aksulu, A.1
Wade, M.2
-
125
-
-
33748796893
-
Open source tools and toolkits for bioinformatics: Significance, and where are we?
-
Stajich, J.E., Lapp, H. Open source tools and toolkits for bioinformatics: Significance, and where are we? Brief. Bioinform. 2006, 7, 287-296.
-
(2006)
Brief. Bioinform.
, vol.7
, pp. 287-296
-
-
Stajich, J.E.1
Lapp, H.2
-
126
-
-
85087152625
-
Jupyter Notebooks-A publishing format for reproducible computational workflows
-
Kluyver, T., Ragan-kelley, B., Pérez, F., Granger, B., Bussonnier, M., Frederic, J., Kelley, K., Hamrick, J., Grout, J., Corlay, S., et al. Jupyter Notebooks-A publishing format for reproducible computational workflows. Position. Power Acad. Publ. Play. Agents Agendas 2016, 87-90.
-
(2016)
Position. Power Acad. Publ. Play. Agents Agendas
, pp. 87-90
-
-
Kluyver, T.1
Ragan-Kelley, B.2
Pérez, F.3
Granger, B.4
Bussonnier, M.5
Frederic, J.6
Kelley, K.7
Hamrick, J.8
Grout, J.9
Corlay, S.10
-
127
-
-
80555140075
-
Scikit-learn: Machine Learning in Python
-
Pedregosa, F., Varoquaux, G., Gramfort, A., Michel, V., Thirion, B., Grisel, O., Blondel, M., Prettenhofer, P., Weiss, R., Dubourg, V., et al. Scikit-learn: Machine Learning in Python. J. Mach. Learn. Res. 2011, 12, 2825-2830.
-
(2011)
J. Mach. Learn. Res.
, vol.12
, pp. 2825-2830
-
-
Pedregosa, F.1
Varoquaux, G.2
Gramfort, A.3
Michel, V.4
Thirion, B.5
Grisel, O.6
Blondel, M.7
Prettenhofer, P.8
Weiss, R.9
Dubourg, V.10
-
128
-
-
84885599052
-
Orange: Data Mining Toolbox in Python
-
Demsar, J., Curk, T., Erjavec, A., Hocevar, T., Milutinovic, M., Mozina, M., Polajnar, M., Toplak, M., Staric, A., Stajdohar, M., et al. Orange: Data Mining Toolbox in Python. J. Mach. Learn. Res. 2013,14, 2349-2353.
-
(2013)
J. Mach. Learn. Res.
, vol.14
, pp. 2349-2353
-
-
Demsar, J.1
Curk, T.2
Erjavec, A.3
Hocevar, T.4
Milutinovic, M.5
Mozina, M.6
Polajnar, M.7
Toplak, M.8
Staric, A.9
Stajdohar, M.10
-
129
-
-
76749092270
-
The WEKA data mining software: An update
-
Hall, M.A., Frank, E., Holmes, G., Pfahringer, B., Reutemann, P., Witten, I.H. The WEKA data mining software: An update. SIGKDD Explor. 2009,11,10-18.
-
(2009)
SIGKDD Explor
, vol.11
, pp. 10-18
-
-
Hall, M.A.1
Frank, E.2
Holmes, G.3
Pfahringer, B.4
Reutemann, P.5
Witten, I.H.6
-
130
-
-
85075670920
-
TensorFlow: A System for Large-Scale Machine Learning TensorFlow: A system for large-scale machine learning
-
Savannah, Georgia, 22 August
-
Abadi, M., Barham, P., Chen, J., Chen, Z., Davis, A., Dean, J., Devin, M., Ghemawat, S., Irving, G., Isard, M., et al. TensorFlow: A System for Large-Scale Machine Learning TensorFlow: A system for large-scale machine learning. In Proceedings of the 12th USENIX Symposium on Operating Systems Design and Implementation (OSDI '16), Savannah, Georgia, 22 August 2016; pp. 265-284.
-
(2016)
Proceedings of the 12Th USENIX Symposium on Operating Systems Design and Implementation (OSDI '16)
, pp. 265-284
-
-
Abadi, M.1
Barham, P.2
Chen, J.3
Chen, Z.4
Davis, A.5
Dean, J.6
Devin, M.7
Ghemawat, S.8
Irving, G.9
Isard, M.10
-
131
-
-
85048351277
-
-
accessed on 23 April
-
Chollet, F. Keras. Available online: https://github.com/fchollet/keras (accessed on 23 April 2018).
-
(2018)
Keras
-
-
Chollet, F.1
-
132
-
-
85047343776
-
Automatic differentiation in PyTorch
-
Paszke, A., Chanan, G., Lin, Z., Gross, S., Yang, E., Antiga, L., Devito, Z. Automatic differentiation in PyTorch. Adv. Neural Inf. Process. Syst. 2017, 30,1-4.
-
(2017)
Adv. Neural Inf. Process. Syst.
, vol.30
, pp. 1-4
-
-
Paszke, A.1
Chanan, G.2
Lin, Z.3
Gross, S.4
Yang, E.5
Antiga, L.6
Devito, Z.7
-
133
-
-
85048348290
-
Microsoft Computational Network Toolkit (CNTK)
-
Palais des Congrès de Montréal: Montréal, QC, Canada
-
Yu, D., Huang, X. Microsoft Computational Network Toolkit (CNTK). In Neural Information Processing Systems (NIPS); Palais des Congrès de Montréal: Montréal, QC, Canada, 2015.
-
Neural Information Processing Systems (NIPS)
, pp. 2015
-
-
Yu, D.1
Huang, X.2
-
134
-
-
84937504995
-
MatConvNet-Convolutional Neural Networks for MATLAB
-
arXiv:1412.4564
-
Vedaldi, A., Lenc, K. MatConvNet-Convolutional Neural Networks for MATLAB. arXiv 2014, arXiv:1412.4564.
-
(2014)
Arxiv
-
-
Vedaldi, A.1
Lenc, K.2
-
135
-
-
85166916238
-
Gephi: An Open Source Software for Exploring and Manipulating Networks
-
San Jose, CA, USA, 17-20 May
-
Bastian, M., Heymann, S., Jacomy, M. Gephi: An Open Source Software for Exploring and Manipulating Networks. In Proceedings of the Third International AAAI Conference on Weblogs and Social Media, San Jose, CA, USA, 17-20 May 2009; pp. 361-362.
-
(2009)
Proceedings of the Third International AAAI Conference on Weblogs and Social Media
, pp. 361-362
-
-
Bastian, M.1
Heymann, S.2
Jacomy, M.3
-
136
-
-
0242490780
-
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
-
Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B., Ideker, T. Cytoscape: A software Environment for integrated models of biomolecular interaction networks. Genome Res. 2003,13, 2498-2504.
-
(2003)
Genome Res
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
-
137
-
-
85017278313
-
The Drug Repurposing Hub: A next-generation drug library and information resource
-
Corsello, S.M., Bittker, J.A., Liu, Z., Gould, J., McCarren, P., Hirschman, J.E., Johnston, S.E., Vrcic, A., Wong, B., Khan, M., et al. The Drug Repurposing Hub: A next-generation drug library and information resource. Nat. Med. 2017, 23, 405-408.
-
(2017)
Nat. Med.
, vol.23
, pp. 405-408
-
-
Corsello, S.M.1
Bittker, J.A.2
Liu, Z.3
Gould, J.4
Mc Carren, P.5
Hirschman, J.E.6
Johnston, S.E.7
Vrcic, A.8
Wong, B.9
Khan, M.10
-
138
-
-
84973365118
-
Cogena, a novel tool for co-expressed gene-set enrichment analysis, applied to drug repositioning and drug mode of action discovery
-
Jia, Z., Liu, Y., Guan, N., Bo, X., Luo, Z., Barnes, M.R. Cogena, a novel tool for co-expressed gene-set enrichment analysis, applied to drug repositioning and drug mode of action discovery. BMC Genomics 2016, 17.
-
(2016)
BMC Genomics
, pp. 17
-
-
Jia, Z.1
Liu, Y.2
Guan, N.3
Bo, X.4
Luo, Z.5
Barnes, M.R.6
-
139
-
-
85026486382
-
Low Data Drug Discovery with One-Shot Learning
-
Altae-Tran, H., Ramsundar, B., Pappu, A.S., Pande, V. Low Data Drug Discovery with One-Shot Learning. ACS Cent. Sci. 2017, 3, 283-293.
-
(2017)
ACS Cent. Sci.
, vol.3
, pp. 283-293
-
-
Altae-Tran, H.1
Ramsundar, B.2
Pappu, A.S.3
Pande, V.4
-
140
-
-
84930959848
-
Comprehensive prediction of drug-protein interactions and side effects for the human proteome
-
Zhou, H., Gao, M., Skolnick, J. Comprehensive prediction of drug-protein interactions and side effects for the human proteome. Sci. Rep. 2015, 5.
-
(2015)
Sci. Rep.
, pp. 5
-
-
Zhou, H.1
Gao, M.2
Skolnick, J.3
-
141
-
-
77954282775
-
E-LEA3D: A computational-aided drug design web server
-
Douguet, D. e-LEA3D: A computational-aided drug design web server. Nucleic Acids Res. 2010,38.
-
(2010)
Nucleic Acids Res.
, pp. 38
-
-
Douguet, D.1
-
142
-
-
77954274184
-
Frog2: Efficient 3D conformation ensemble generator for small compounds
-
Miteva, M.A., Guyon, F., Tufféry, P. Frog2: Efficient 3D conformation ensemble generator for small compounds. Nucleic Acids Res. 2010, 38.
-
(2010)
Nucleic Acids Res.
, pp. 38
-
-
Miteva, M.A.1
Guyon, F.2
Tufféry, P.3
-
143
-
-
84943620492
-
Global optimization-based inference of chemogenomic features from drug-target interactions
-
Zu, S., Chen, T., Li, S. Global optimization-based inference of chemogenomic features from drug-target interactions. Bioinformatics 2015, 31, 2523-2529.
-
(2015)
Bioinformatics
, vol.31
, pp. 2523-2529
-
-
Zu, S.1
Chen, T.2
Li, S.3
-
144
-
-
84971013934
-
Data integration to prioritize drugs using genomics and curated data
-
Louhimo, R., Laakso, M., Belitskin, D., Klefström, J., Lehtonen, R., Hautaniemi, S. Data integration to prioritize drugs using genomics and curated data. BioData Min. 2016, 9.
-
(2016)
Biodata Min.
, pp. 9
-
-
Louhimo, R.1
Laakso, M.2
Belitskin, D.3
Klefström, J.4
Lehtonen, R.5
Hautaniemi, S.6
-
145
-
-
0037361967
-
The Chemistry Development Kit (CDK): An open-source Java library for chemo-and bioinformatics
-
Steinbeck, C., Han, Y., Kuhn, S., Horlacher, O., Luttmann, E., Willighagen, E. The Chemistry Development Kit (CDK): An open-source Java library for chemo-and bioinformatics. J. Chem. Inf. Comput. Sci. 2003, 43, 493-500.
-
(2003)
J. Chem. Inf. Comput. Sci.
, vol.43
, pp. 493-500
-
-
Steinbeck, C.1
Han, Y.2
Kuhn, S.3
Horlacher, O.4
Luttmann, E.5
Willighagen, E.6
-
146
-
-
85020403526
-
L1000CDS2: LINCS L1000 characteristic direction signatures search engine
-
Duan, Q., Reid, S.P., Clark, N.R., Wang, Z., Fernandez, N.F., Rouillard, A.D., Readhead, B., Tritsch, S.R., Hodos, R., Hafner, M., et al. L1000CDS2: LINCS L1000 characteristic direction signatures search engine. NPJ Syst. Biol. Appl. 2016, 2,16015.
-
(2016)
NPJ Syst. Biol. Appl.
, vol.2
, pp. 16015
-
-
Duan, Q.1
Reid, S.P.2
Clark, N.R.3
Wang, Z.4
Fernandez, N.F.5
Rouillard, A.D.6
Readhead, B.7
Tritsch, S.R.8
Hodos, R.9
Hafner, M.10
-
147
-
-
84902007424
-
Mantra 2.0: An online collaborative resource for drug mode of action and repurposing by network analysis
-
Carrella, D., Napolitano, F., Rispoli, R., Miglietta, M., Carissimo, A., Cutillo, L., Sirci, F., Gregoretti, F., Di Bernardo, D. Mantra 2.0: An online collaborative resource for drug mode of action and repurposing by network analysis. Bioinformatics2014, 30,1787-1788.
-
Bioinformatics2014
, vol.30
, pp. 1787-1788
-
-
Carrella, D.1
Napolitano, F.2
Rispoli, R.3
Miglietta, M.4
Carissimo, A.5
Cutillo, L.6
Sirci, F.7
Gregoretti, F.8
Di Bernardo, D.9
-
148
-
-
80053512597
-
Open Babel: An Open chemical toolbox
-
O'Boyle, N.M., Banck, M., James, C.A., Morley, C., Vandermeersch, T., Hutchison, G.R. Open Babel: An Open chemical toolbox. J. Cheminform. 2011, 3.
-
(2011)
J. Cheminform.
, pp. 3
-
-
O'boyle, N.M.1
Banck, M.2
James, C.A.3
Morley, C.4
Vandermeersch, T.5
Hutchison, G.R.6
-
149
-
-
84868138829
-
Open PHACTS: Semantic interoperability for drug discovery
-
Williams, A.J., Harland, L., Groth, P., Pettifer, S., Chichester, C., Willighagen, E.L., Evelo, C.T., Blomberg, N., Ecker, G., Goble, C., et al. Open PHACTS: Semantic interoperability for drug discovery. Drug Discov. Today 2012,17,1188-1198.
-
(2012)
Drug Discov. Today
, vol.17
, pp. 1188-1198
-
-
Williams, A.J.1
Harland, L.2
Groth, P.3
Pettifer, S.4
Chichester, C.5
Willighagen, E.L.6
Evelo, C.T.7
Blomberg, N.8
Ecker, G.9
Goble, C.10
-
150
-
-
0040235325
-
The Who and Why of ISI
-
accessed on 1 June 2018
-
Garfield, E. The Who and Why of ISI. Essays of Information Scientist. 1966. Available online: http://garfield. library.upenn.edu/essays/V1p033y1962-73.pdf (accessed on 1 June 2018).
-
(1966)
Essays of Information Scientist.
-
-
Garfield, E.1
-
151
-
-
84865117327
-
-
Repeat after me
-
Repeat after me. Nature 2012, 488, 253.
-
(2012)
Nature
, vol.488
, pp. 253
-
-
-
152
-
-
84859169880
-
Drug development: Raise standards for preclinical cancer research
-
Begley, C.G., Ellis, L.M. Drug development: Raise standards for preclinical cancer research. Nature 2012, 483, 531-533.
-
(2012)
Nature
, vol.483
, pp. 531-533
-
-
Begley, C.G.1
Ellis, L.M.2
-
153
-
-
85019914914
-
Irreproducible biology research costs put at $28 billion per year
-
Baker, M. Irreproducible biology research costs put at $28 billion per year. Nature 2015.
-
(2015)
Nature
-
-
Baker, M.1
-
154
-
-
82755174123
-
Reproducible research in computational science
-
Peng, R.D. Reproducible research in computational science. Science 2011, 334, 1226-1227.
-
(2011)
Science
, vol.334
, pp. 1226-1227
-
-
Peng, R.D.1
-
155
-
-
18544387899
-
Reproducible Research: A Bioinformatics Case Study
-
Gentleman, R. Reproducible Research: A Bioinformatics Case Study. Stat. Appl. Genet. Mol. Biol. 2005, 4.
-
(2005)
Stat. Appl. Genet. Mol. Biol.
, pp. 4
-
-
Gentleman, R.1
-
156
-
-
85024396369
-
Reproducible Drug Repurposing: When Similarity Does Not Suffice
-
Guney, E. Reproducible Drug Repurposing: When Similarity Does Not Suffice. Pac. Symp. Biocomput. 2016, 22,132-143.
-
(2016)
Pac. Symp. Biocomput.
, vol.22
, pp. 132-143
-
-
Guney, E.1
-
157
-
-
84962269370
-
The FAIR Guiding Principles for scientific data management and stewardship
-
Wilkinson, M.D., Dumontier, M., Aalbersberg, I.J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., da Silva Santos, L.B., Bourne, P.E., et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci. Data 2016, 3,160018.
-
(2016)
Sci. Data
, vol.3
, pp. 160018
-
-
Wilkinson, M.D.1
Dumontier, M.2
Aalbersberg, I.J.3
Appleton, G.4
Axton, M.5
Baak, A.6
Blomberg, N.7
Boiten, J.-W.8
Da Silva Santos, L.B.9
Bourne, P.E.10
-
158
-
-
85042658326
-
Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses
-
Torre, D., Krawczuk, P., Jagodnik, K.M., Lachmann, A., Wang, Z., Wang, L., Kuleshov, M.V., Ma'Ayan, A. Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses. Sci. Data 2018,5.
-
(2018)
Sci. Data
, pp. 5
-
-
Torre, D.1
Krawczuk, P.2
Jagodnik, K.M.3
Lachmann, A.4
Wang, Z.5
Wang, L.6
Kuleshov, M.V.7
Ma'ayan, A.8
-
159
-
-
84874350660
-
Git can facilitate greater reproducibility and increased transparency in science
-
Ram, K. Git can facilitate greater reproducibility and increased transparency in science. Source Code Biol. Med. 2013, 8.
-
(2013)
Source Code Biol. Med.
, pp. 8
-
-
Ram, K.1
-
160
-
-
84926444656
-
Docker: Lightweight Linux containers for consistent development and deployment
-
Merkel, D. Docker: Lightweight Linux containers for consistent development and deployment. Linux J. 2014, 2014, 2.
-
(2014)
Linux J
, vol.2014
, pp. 2
-
-
Merkel, D.1
|