-
1
-
-
84875227396
-
Signalling bias in new drug discovery: Detection, quantification and therapeutic impact
-
Kenakin T, Christopoulos A. 2013. Signalling bias in new drug discovery: detection, quantification and therapeutic impact. Nat. Rev. Drug Discov. 12:205-16
-
(2013)
Nat. Rev. Drug Discov.
, vol.12
, pp. 205-216
-
-
Kenakin, T.1
Christopoulos, A.2
-
2
-
-
81755184126
-
Allo-network drugs: Harnessing allostery in cellular networks
-
Nussinov R, Tsai CJ, Csermely P. 2011. Allo-network drugs: harnessing allostery in cellular networks. Trends Pharmacol. Sci. 32:686-93
-
(2011)
Trends Pharmacol. Sci.
, vol.32
, pp. 686-693
-
-
Nussinov, R.1
Tsai, C.J.2
Csermely, P.3
-
3
-
-
84855882587
-
Novel computational approaches to polypharmacology as a means to define responses to individual drugs
-
Xie L, Kinnings SL, Bourne PE. 2012. Novel computational approaches to polypharmacology as a means to define responses to individual drugs. Annu. Rev. Pharmacol. Toxicol. 52:361-79
-
(2012)
Annu. Rev. Pharmacol. Toxicol.
, vol.52
, pp. 361-379
-
-
Xie, L.1
Kinnings, S.L.2
Bourne, P.E.3
-
4
-
-
79955562721
-
Drug discovery using chemical systems biology: Weak inhibition of multiple kinases may contribute to the anti-cancer effect of Nelfinavir
-
Xie L, Evangelidis T, Xie L, Bourne PE. 2011. Drug discovery using chemical systems biology: weak inhibition of multiple kinases may contribute to the anti-cancer effect of Nelfinavir. PLOS Comput. Biol. 7:e1002037
-
(2011)
PLOS Comput. Biol.
, vol.7
, pp. e1002037
-
-
Xie, L.1
Evangelidis, T.2
Xie, L.3
Bourne, P.E.4
-
5
-
-
84855906454
-
Systems pharmacology: Network analysis to identify multiscale mechanisms of drug action
-
Zhao S, Iyengar R. 2012. Systems pharmacology: network analysis to identify multiscale mechanisms of drug action. Annu. Rev. Pharmacol. Toxicol. 52:505-21
-
(2012)
Annu. Rev. Pharmacol. Toxicol.
, vol.52
, pp. 505-521
-
-
Zhao, S.1
Iyengar, R.2
-
6
-
-
84901675919
-
Towards structural systems pharmacology to study complex disease and personalized medicine
-
Xie L, Ge X, Tan H, Xie L, Zhang YL, et al. 2014. Towards structural systems pharmacology to study complex disease and personalized medicine. PLOS Comput. Biol. 10:e1003554
-
(2014)
PLOS Comput. Biol.
, vol.10
, pp. e1003554
-
-
Xie, L.1
Ge, X.2
Tan, H.3
Xie, L.4
Zhang, Y.L.5
-
7
-
-
85009063274
-
-
White Pap., QSP Workshop Group, Natl. Inst. Health, Bethesda, MD.
-
Sorger PK, Allerheiligen SRB, Abernethy DR, Altman RB, Brouwer KLR, et al. 2011. Quantitative and systems pharmacology in the post-genomic era: new approaches to discovering drugs and understanding therapeutic mechanisms. White Pap., QSP Workshop Group, Natl. Inst. Health, Bethesda, MD. https://www. nigms.nih.gov/Training/Documents/SystemsPharmaWPSorger2011.pdf
-
(2011)
Quantitative and Systems Pharmacology in the Post-genomic Era: New Approaches to Discovering Drugs and Understanding Therapeutic Mechanisms
-
-
Sorger, P.K.1
Allerheiligen, S.R.B.2
Abernethy, D.R.3
Altman, R.B.4
Brouwer, K.L.R.5
-
8
-
-
84897487215
-
Turning the Titanic
-
Zerhouni EA. 2014. Turning the Titanic. Sci. Transl. Med. 6:221ed2
-
(2014)
Sci. Transl. Med.
, vol.6
, pp. 221ed2
-
-
Zerhouni, E.A.1
-
9
-
-
84961371413
-
Lean Big Data integration in systems biology and systems pharmacology
-
Ma'ayan A, Rouillard AD, Clark NR, Wang Z, Duan Q, Kou Y. 2014. Lean Big Data integration in systems biology and systems pharmacology. Trends Pharmacol. Sci. 35:450-60
-
(2014)
Trends Pharmacol. Sci.
, vol.35
, pp. 450-460
-
-
Ma'Ayan, A.1
Rouillard, A.D.2
Clark, N.R.3
Wang, Z.4
Duan, Q.5
Kou, Y.6
-
10
-
-
84958678820
-
Providing data science support for systems pharmacology and its implications to drug discovery
-
Hart T, Xie L. 2015. Providing data science support for systems pharmacology and its implications to drug discovery. Expert Opin. Drug Discov. 11:241-56
-
(2015)
Expert Opin. Drug Discov.
, vol.11
, pp. 241-256
-
-
Hart, T.1
Xie, L.2
-
11
-
-
84946227707
-
Perspective: Sustaining the big-data ecosystem
-
Bourne PE, Lorsch JR, Green ED. 2015. Perspective: sustaining the big-data ecosystem. Nature 527:S16-17
-
(2015)
Nature
, vol.527
, pp. S16-17
-
-
Bourne, P.E.1
Lorsch, J.R.2
Green, E.D.3
-
12
-
-
68249144628
-
Drug discovery using chemical systems biology: Repositioning the safemedicineComtan to treat multi-drug and extensively drug resistant tuberculosis
-
Kinnings SL, Liu N, Buchmeier N, Tonge PJ, Xie L, Bourne PE. 2009. Drug discovery using chemical systems biology: repositioning the safemedicineComtan to treat multi-drug and extensively drug resistant tuberculosis. PLOS Comput. Biol. 5:e1000423
-
(2009)
PLOS Comput. Biol.
, vol.5
, pp. e1000423
-
-
Kinnings, S.L.1
Liu, N.2
Buchmeier, N.3
Tonge, P.J.4
Xie, L.5
Bourne, P.E.6
-
13
-
-
84901650505
-
Anti-infectious drug repurposing using an integrated chemical genomics and structural systems biology approach
-
Kohala Coast, Hawaii, Jan. 3-7
-
Ng C, Hauptman R, Zhang Y, Bourne PE, Xie L. 2014. Anti-infectious drug repurposing using an integrated chemical genomics and structural systems biology approach. Proc. Pac. Symp. Biocomput., Kohala Coast, Hawaii, Jan. 3-7, pp. 136-47
-
(2014)
Proc. Pac. Symp. Biocomput.
, pp. 136-147
-
-
Ng, C.1
Hauptman, R.2
Zhang, Y.3
Bourne, P.E.4
Xie, L.5
-
14
-
-
84864583593
-
Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence
-
HoSui SJ, Lo R, Fernandes AR, Caulfield MDG, Lerman JA, et al. 2012. Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence. Int. J. Antimicrob. Agents 40:246-51
-
(2012)
Int. J. Antimicrob. Agents
, vol.40
, pp. 246-251
-
-
Ho Sui, S.J.1
Lo, R.2
Fernandes, A.R.3
Caulfield, M.D.4
Glerman, J.A.5
-
18
-
-
67049100457
-
Drug discovery using chemical systems biology: Identification of the protein-ligand binding network to explain the side effects of CETP inhibitors
-
Xie L, Li J, Xie L, Bourne PE. 2009. Drug discovery using chemical systems biology: identification of the protein-ligand binding network to explain the side effects of CETP inhibitors. PLOS Comput. Biol. 5:e1000387
-
(2009)
PLOS Comput. Biol.
, vol.5
, pp. e1000387
-
-
Xie, L.1
Li, J.2
Xie, L.3
Bourne, P.E.4
-
19
-
-
84885441247
-
Systems pharmacology of adverse event mitigation by drug combinations
-
Zhao S, Nishimura T, Chen Y, Azeloglu EU, GottesmanO, et al. 2013. Systems pharmacology of adverse event mitigation by drug combinations. Sci. Transl. Med. 5:206ra140
-
(2013)
Sci. Transl. Med.
, vol.5
, pp. 206ra140
-
-
Zhao, S.1
Nishimura, T.2
Chen, Y.3
Azeloglu, E.U.4
Gottesman, O.5
-
20
-
-
84951056186
-
Personalized whole-cell kinetic models of metabolism for discovery in genomics and pharmacodynamics
-
Bordbar A, McCloskey D, Zielinski DC, Sonnenschein N, Jamshidi N, Palsson BO. 2015. Personalized whole-cell kinetic models of metabolism for discovery in genomics and pharmacodynamics. Cell Syst. 1:283-92
-
(2015)
Cell Syst.
, vol.1
, pp. 283-292
-
-
Bordbar, A.1
McCloskey, D.2
Zielinski, D.C.3
Sonnenschein, N.4
Jamshidi, N.5
Palsson, B.O.6
-
21
-
-
35148838537
-
Drug-target network
-
Yildirim MA, Goh KI, Cusick ME, Barabasi AL, Vidal M. 2007. Drug-target network. Nat. Biotechnol. 25:1119-26
-
(2007)
Nat. Biotechnol.
, vol.25
, pp. 1119-1126
-
-
Yildirim, M.A.1
Goh, K.I.2
Cusick, M.E.3
Barabasi, A.L.4
Vidal, M.5
-
22
-
-
78649661569
-
The Mycobacterium tuberculosis drugome and its polypharmacological implications
-
Kinnings SL, Xie L, Fung K, Xie L, Bourne PE. 2010. The Mycobacterium tuberculosis drugome and its polypharmacological implications. PLOS Comput. Biol. 6:e100976
-
(2010)
PLOS Comput. Biol.
, vol.6
, pp. e100976
-
-
Kinnings, S.L.1
Xie, L.2
Fung, K.3
Xie, L.4
Bourne, P.E.5
-
23
-
-
84892788440
-
Constraint-based models predict metabolic and associated cellular functions
-
Bordbar A, Monk JM, King ZA, Palsson BO. 2014. Constraint-based models predict metabolic and associated cellular functions. Nat. Rev. Genet. 15:107-20
-
(2014)
Nat. Rev. Genet.
, vol.15
, pp. 107-120
-
-
Bordbar, A.1
Monk, J.M.2
King, Z.A.3
Palsson, B.O.4
-
24
-
-
54049114302
-
Virtual cell modelling and simulation software environment
-
Moraru II, Schaff JC, Slepchenko BM, Blinov ML, Morgan F, et al. 2008. Virtual cell modelling and simulation software environment. IET Syst. Biol. 2:352-62
-
(2008)
IET Syst. Biol.
, vol.2
, pp. 352-362
-
-
Moraru, I.I.1
Schaff, J.C.2
Slepchenko, B.M.3
Blinov, M.L.4
Morgan, F.5
-
26
-
-
84896721689
-
Quantifying reproducibility in computational biology: The case of the tuberculosis drugome
-
Garijo D, Kinnings SL, Xie L, Xie L, Zhang YL, et al. 2013. Quantifying reproducibility in computational biology: the case of the tuberculosis drugome. PLOS ONE 8:e80278
-
(2013)
PLOS ONE
, vol.8
, pp. e80278
-
-
Garijo, D.1
Kinnings, S.L.2
Xie, L.3
Xie, L.4
Zhang, Y.L.5
-
28
-
-
13444270892
-
The RCSB Protein Data Bank: A redesigned query system and relational database based on the mmCIF schema
-
Deshpande N, Addess KJ, Bluhm WF, Merino-Ott JC, Townsend-Merino W, et al. 2005. The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res. 33:D233-37
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. D233-D237
-
-
Deshpande, N.1
Addess, K.J.2
Bluhm, W.F.3
Merino-Ott, J.C.4
Townsend-Merino, W.5
-
29
-
-
84862192766
-
ChEMBL: A large-scale bioactivity database for drug discovery
-
Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, et al. 2012. ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res. 40:D1100-7
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D1100-D1107
-
-
Gaulton, A.1
Bellis, L.J.2
Bento, A.P.3
Chambers, J.4
Davies, M.5
-
30
-
-
13444273448
-
The universal protein resource (UniProt)
-
Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, et al. 2005. The Universal Protein Resource (UniProt). Nucleic Acids Res. 33:D154-59
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. D154-D159
-
-
Bairoch, A.1
Apweiler, R.2
Wu, C.H.3
Barker, W.C.4
Boeckmann, B.5
-
31
-
-
84912569105
-
An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models
-
Chindelevitch L, Trigg J, Regev A, Berger B. 2014. An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models. Nat. Commun. 5:4893
-
(2014)
Nat. Commun.
, vol.5
, pp. 4893
-
-
Chindelevitch, L.1
Trigg, J.2
Regev, A.3
Berger, B.4
-
32
-
-
84879920277
-
Compressive genomics for protein databases
-
Daniels NM, Gallant A, Peng J, Cowen LJ, Baym M, Berger B. 2013. Compressive genomics for protein databases. Bioinformatics 29:i283-90
-
(2013)
Bioinformatics
, vol.29
, pp. i283-i290
-
-
Daniels, N.M.1
Gallant, A.2
Peng, J.3
Cowen, L.J.4
Baym, M.5
Berger, B.6
-
35
-
-
84942814743
-
The widening gulf between genomics data generation and consumption: A practical guide to big data transfer technology
-
Feltus FA, Breen JR III, Deng J, Izard RS, Konger CA, et al. 2015. The widening gulf between genomics data generation and consumption: a practical guide to big data transfer technology. Bioinform. Biol. Insights 2015(Suppl. 1):9-19
-
(2015)
Bioinform. Biol. Insights
, vol.2015
, pp. 9-19
-
-
Feltus, F.A.1
Breen, J.R.2
Deng, J.3
Izard, R.S.4
Konger, C.A.5
-
36
-
-
84991905414
-
Improving collaboration by standardization efforts in systems biology
-
Drager A, Palsson BO. 2014. Improving collaboration by standardization efforts in systems biology. Front. Bioeng. Biotechnol. 2:61
-
(2014)
Front. Bioeng. Biotechnol.
, vol.2
, pp. 61
-
-
Drager, A.1
Palsson, B.O.2
-
38
-
-
45749118607
-
Promoting coherentminimum reporting guidelines for biological and biomedical investigations: The MIBBI project
-
Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, et al. 2008. Promoting coherentminimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat. Biotechnol. 26:889-96
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 889-896
-
-
Taylor, C.F.1
Field, D.2
Sansone, S.A.3
Aerts, J.4
Apweiler, R.5
-
39
-
-
28644433993
-
Minimum information requested in the annotation of biochemical models (MIRIAM)
-
Le Novère N, Finney A, Hucka M, Bhalla US, Campagne F, et al. 2005. Minimum information requested in the annotation of biochemical models (MIRIAM). Nat. Biotechnol. 23:1509-15
-
(2005)
Nat. Biotechnol.
, vol.23
, pp. 1509-1515
-
-
Le Novère, N.1
Finney, A.2
Hucka, M.3
Bhalla, U.S.4
Campagne, F.5
-
40
-
-
84862156032
-
Identifiers.org and MIRIAM Registry: Community resources to provide persistent identification
-
Juty N, Le Novère N, Laibe C. 2012. Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. Nucleic Acids Res. 40:D580-86
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D580-D586
-
-
Juty, N.1
Le Novère, N.2
Laibe, C.3
-
41
-
-
40349100409
-
MIRIAM Resources: Tools to generate and resolve robust cross-references in Systems Biology
-
Laibe C, Le Novère N. 2007. MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology. BMC Syst. Biol. 1:58
-
(2007)
BMC Syst. Biol.
, vol.1
, pp. 58
-
-
Laibe, C.1
Le Novère, N.2
-
42
-
-
84936749645
-
Pharmacometrics Markup Language (PharmML): Opening new perspectives for model exchange in drug development
-
Swat MJ, Moodie S, Wimalaratne SM, Kristensen NR, Lavielle M, et al. 2015. Pharmacometrics Markup Language (PharmML): opening new perspectives for model exchange in drug development. CPT Pharmacomet. Syst. Pharmacol. 4:316-19
-
(2015)
CPT Pharmacomet. Syst. Pharmacol.
, vol.4
, pp. 316-319
-
-
Swat, M.J.1
Moodie, S.2
Wimalaratne, S.M.3
Kristensen, N.R.4
Lavielle, M.5
-
43
-
-
77955801615
-
Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
-
Goecks J, Nekrutenko A, Taylor J. 2010. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11:R86
-
(2010)
Genome Biol.
, vol.11
, pp. R86
-
-
Goecks, J.1
Nekrutenko, A.2
Taylor, J.3
-
45
-
-
84945933008
-
Do genome-scale models need exact solvers or clearer standards
-
Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, et al. 2015. Do genome-scale models need exact solvers or clearer standards Mol. Syst. Biol. 11:831
-
(2015)
Mol. Syst. Biol.
, vol.11
, pp. 831
-
-
Ebrahim, A.1
Almaas, E.2
Bauer, E.3
Bordbar, A.4
Burgard, A.P.5
-
46
-
-
84945937607
-
Reply to Do genome-scale models need exact solvers or clearer standards
-
Chindelevitch L, Trigg J, Regev A, Berger B. 2015. Reply to "Do genome-scale models need exact solvers or clearer standards" Mol. Syst. Biol. 11:830
-
(2015)
Mol. Syst. Biol.
, vol.11
, pp. 830
-
-
Chindelevitch, L.1
Trigg, J.2
Regev, A.3
Berger, B.4
-
47
-
-
78049445175
-
Drug off-target effects predicted using structural analysis in the context of a metabolic network model
-
Chang RL, Xie L, Xie L, Bourne PE, Palsson B. 2010. Drug off-target effects predicted using structural analysis in the context of a metabolic network model. PLOS Comput. Biol. 6:e1000938
-
(2010)
PLOS Comput. Biol.
, vol.6
, pp. e1000938
-
-
Chang, R.L.1
Xie, L.2
Xie, L.3
Bourne, P.E.4
Palsson, B.5
-
48
-
-
84885147536
-
Antibacterial mechanisms identified through structural systems pharmacology
-
Chang RL, Xie L, Bourne PE, Palsson BO. 2013. Antibacterial mechanisms identified through structural systems pharmacology. BMC Syst. Biol. 7:102
-
(2013)
BMC Syst. Biol.
, vol.7
, pp. 102
-
-
Chang, R.L.1
Xie, L.2
Bourne, P.E.3
Palsson, B.O.4
-
49
-
-
84867554554
-
Predicting drug targets and biomarkers of cancer via genome-scale metabolic modeling
-
Jerby L, Ruppin E. 2012. Predicting drug targets and biomarkers of cancer via genome-scale metabolic modeling. Clin. Cancer Res. 18:5572-84
-
(2012)
Clin. Cancer Res.
, vol.18
, pp. 5572-5584
-
-
Jerby, L.1
Ruppin, E.2
-
50
-
-
79955570036
-
Minimum Information about a Simulation Experiment (MIASE)
-
Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, et al. 2011. Minimum Information About a Simulation Experiment (MIASE). PLOS Comput. Biol. 7:e1001122
-
(2011)
PLOS Comput. Biol.
, vol.7
, pp. e1001122
-
-
Waltemath, D.1
Adams, R.2
Beard, D.A.3
Bergmann, F.T.4
Bhalla, U.S.5
-
51
-
-
0037365194
-
Active learning with support vector machines in the drug discovery process
-
Warmuth MK, Liao J, Rätsch G, Mathieson M, Putta S, Lemmen C. 2003. Active learning with support vector machines in the drug discovery process. J. Chem. Inf. Comput. Sci. 43:667-73
-
(2003)
J. Chem. Inf. Comput. Sci.
, vol.43
, pp. 667-673
-
-
Warmuth, M.K.1
Liao, J.2
Rätsch, G.3
Mathieson, M.4
Putta, S.5
Lemmen, C.6
-
52
-
-
84959903087
-
PDID: Database of molecular-level putative protein-drug interactions in the structural human proteome
-
Wang C, Hu G, Wang K, Brylinski M, Xie L, Kurgan L. 2015. PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. Bioinformatics 32:579-86
-
(2015)
Bioinformatics
, vol.32
, pp. 579-586
-
-
Wang, C.1
Hu, G.2
Wang, K.3
Brylinski, M.4
Xie, L.5
Kurgan, L.6
-
53
-
-
84976877544
-
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models
-
King ZA, Lu J, Drager A, Miller P, Federowicz S, et al. 2016. BiGG Models: a platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Res. 44:D515-22
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D515-D522
-
-
King, Z.A.1
Lu, J.2
Drager, A.3
Miller, P.4
Federowicz, S.5
-
54
-
-
84881185232
-
Drug and disease model resources: A consortium to create standards and tools to enhance model-based drug development
-
Harnisch L, Matthews I, Chard J, KarlssonMO. 2013. Drug and disease model resources: a consortium to create standards and tools to enhance model-based drug development. CPT Pharmacomet. Syst. Pharmacol. 2:e34
-
(2013)
CPT Pharmacomet. Syst. Pharmacol.
, vol.2
, pp. e34
-
-
Harnisch, L.1
Matthews, I.2
Chard, J.3
Karlsson, M.O.4
-
55
-
-
84856277549
-
Developing predictive molecular maps of human disease through community-based modeling
-
Derry JM, Mangravite LM, Suver C, FuriaMD, Henderson D, et al. 2012. Developing predictive molecular maps of human disease through community-based modeling. Nat. Genet. 44:127-30
-
(2012)
Nat. Genet.
, vol.44
, pp. 127-130
-
-
Derry, J.M.1
Mangravite, L.M.2
Suver, C.3
Furia, M.D.4
Henderson, D.5
-
56
-
-
0030196364
-
Stacked regressions
-
Breiman L. 1996. Stacked regressions. Mach. Learn. 24:49-64
-
(1996)
Mach. Learn.
, vol.24
, pp. 49-64
-
-
Breiman, L.1
-
57
-
-
84885173138
-
Collective judgment predicts disease-associated single nucleotide variants
-
Capriotti E, Altman RB, Bromberg Y. 2013. Collective judgment predicts disease-associated single nucleotide variants. BMC Genom. 14(Suppl. 3):S2
-
(2013)
BMC Genom.
, vol.14
, pp. S2
-
-
Capriotti, E.1
Altman, R.B.2
Bromberg, Y.3
-
58
-
-
80053437179
-
Multimodal deep learning
-
Ngiam J, Khosla A, Kim M, Nam J, Lee H, Ng AY. 2011. Multimodal deep learning. Proc. 28th Int. Conf. Mach. Learn. (ICML-11), pp. 689-96
-
(2011)
Proc. 28th Int. Conf. Mach. Learn. (ICML-11)
, pp. 689-696
-
-
Ngiam, J.1
Khosla, A.2
Kim, M.3
Nam, J.4
Lee, H.5
Ng, A.Y.6
-
59
-
-
84906549588
-
A community effort to assess and improve drug sensitivity prediction algorithms
-
Costello JC, Heiser LM, Georgii E, Gonen M, Menden MP, et al. 2014. A community effort to assess and improve drug sensitivity prediction algorithms. Nat. Biotechnol. 32:1202-12
-
(2014)
Nat. Biotechnol.
, vol.32
, pp. 1202-1212
-
-
Costello, J.C.1
Heiser, L.M.2
Georgii, E.3
Gonen, M.4
Menden, M.P.5
-
60
-
-
84866459051
-
Predicting drug-target interactions from chemical and genomic kernels using Bayesian matrix factorization
-
Gonen M. 2012. Predicting drug-target interactions from chemical and genomic kernels using Bayesian matrix factorization. Bioinformatics 28:2304-10
-
(2012)
Bioinformatics
, vol.28
, pp. 2304-2310
-
-
Gonen, M.1
-
61
-
-
84866436691
-
PARADIGM-SHIFTpredicts the function of mutations in multiple cancers using pathway impact analysis
-
Ng S, Collisson EA, Sokolov A, Goldstein T, Gonzalez-Perez A, et al. 2012. PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis. Bioinformatics 28:i640-46
-
(2012)
Bioinformatics
, vol.28
, pp. i640-i646
-
-
Ng, S.1
Collisson, E.A.2
Sokolov, A.3
Goldstein, T.4
Gonzalez-Perez, A.5
-
62
-
-
84880848367
-
Inferring multi-target QSAR models with taxonomy-based multi-task learning
-
Rosenbaum L, Dorr A, Bauer MR, Boeckler FM, Zell A. 2013. Inferring multi-target QSAR models with taxonomy-based multi-task learning. J. Cheminformatics 5:33
-
(2013)
J. Cheminformatics
, vol.5
, pp. 33
-
-
Rosenbaum, L.1
Dorr, A.2
Bauer, M.R.3
Boeckler, F.M.4
Zell, A.5
-
63
-
-
77955032649
-
PLANET: Massively parallel learning of tree ensembles with MapReduce
-
Aug. 24-28, Lyon, Fr. 1426-37
-
Panda B, Herbach JS, Basu S, Bayardo RJ. 2009. PLANET: massively parallel learning of tree ensembles with MapReduce. Proc. VLDB '09, Aug. 24-28, Lyon, Fr., pp. 1426-37
-
(2009)
Proc. VLDB '09
-
-
Panda, B.1
Herbach, J.S.2
Basu, S.3
Bayardo, R.J.4
-
64
-
-
84865330735
-
Scalable and parallel boosting with MapReduce
-
Palit I, Reddy CK. 2012. Scalable and parallel boosting with MapReduce. Knowl. Data Eng. IEEE Trans. 24:1904-16
-
(2012)
Knowl. Data Eng. IEEE Trans.
, vol.24
, pp. 1904-1916
-
-
Palit, I.1
Reddy, C.K.2
-
65
-
-
84958074030
-
Schizophrenia risk from complex variation of complement component 4
-
Sekar A, Bialas AR, de Rivera H, Davis A, Hammond TR, et al. 2016. Schizophrenia risk from complex variation of complement component 4. Nature 530:177-83
-
(2016)
Nature
, vol.530
, pp. 177-183
-
-
Sekar, A.1
Bialas, A.R.2
De Rivera, H.3
Davis, A.4
Hammond, T.R.5
-
66
-
-
84964240053
-
Biological and therapeutic impact of intratumor heterogeneity in cancer evolution
-
McGranahan N, Swanton C. 2015. Biological and therapeutic impact of intratumor heterogeneity in cancer evolution. Cancer Cell 27:15-26
-
(2015)
Cancer Cell
, vol.27
, pp. 15-26
-
-
McGranahan, N.1
Swanton, C.2
-
68
-
-
83555170269
-
Random classification noise defeats all convex potential boosters
-
Long PM, Servedio RA. 2010. Random classification noise defeats all convex potential boosters. Mach. Learn. 78:287-304
-
(2010)
Mach. Learn.
, vol.78
, pp. 287-304
-
-
Long, P.M.1
Servedio, R.A.2
-
70
-
-
84988429118
-
Multi-view ensemble learning: An optimal feature set partitioning for highdimensional data classification
-
Kumar V, Minz S. 2015. Multi-view ensemble learning: an optimal feature set partitioning for highdimensional data classification. Knowledge Inf. Syst. 2015:1-59
-
(2015)
Knowledge Inf. Syst.
, vol.2015
, pp. 1-59
-
-
Kumar, V.1
Minz, S.2
-
71
-
-
0028401306
-
Case-based reasoning: Foundational issues, methodological variations, and system approaches
-
Aamodt A, Plaza E. 1994. Case-based reasoning: foundational issues, methodological variations, and system approaches. Artif. Intell. Commun. 7:39-59
-
(1994)
Artif. Intell. Commun.
, vol.7
, pp. 39-59
-
-
Aamodt, A.1
Plaza, E.2
-
72
-
-
84884504655
-
Multi-agent, multi-case-based reasoning
-
ed. B Diáz-Agudo, IWatson Berlin: Springer
-
Epstein SL, Yun X, Xie L. 2012. Multi-agent, multi-case-based reasoning. In Case-Based Reasoning Research and Development: International Conference on Case-Based Reasoning 2012, ed. B Diáz-Agudo, IWatson, pp. 74-88. Berlin: Springer
-
(2012)
Case-Based Reasoning Research and Development: International Conference on Case-Based Reasoning 2012
, pp. 74-88
-
-
Epstein, S.L.1
Yun, X.2
Xie, L.3
-
73
-
-
84877044583
-
Explanation and reliability of individual predictions
-
Kononenko I, Strumbelj E, Bosnic Z, Pevec D, Kukar M, Robnik-Sikonja M. 2013. Explanation and reliability of individual predictions. Informatica 37:41-48
-
(2013)
Informatica
, vol.37
, pp. 41-48
-
-
Kononenko, I.1
Strumbelj, E.2
Bosnic, Z.3
Pevec, D.4
Kukar, M.5
Robnik-Sikonja, M.6
-
74
-
-
84948778960
-
Transductive reliability estimation for individual classifications
-
ed.HDai, JN Liu, E Smirnov Cham, Switz.: Springer
-
Kukar M. 2012. Transductive reliability estimation for individual classifications. In Machine Learning and DataMining: Reliable Knowledge Discovery, ed.HDai, JN Liu, E Smirnov, pp. 3-27. Cham, Switz.: Springer
-
(2012)
Machine Learning and DataMining: Reliable Knowledge Discovery
, pp. 3-27
-
-
Kukar, M.1
-
75
-
-
84911005528
-
Random Prism: A noise-tolerant alternative to Random Forests
-
Stahl F, Bramer M. 2014. Random Prism: a noise-tolerant alternative to Random Forests. Expert Syst. 31:411-20
-
(2014)
Expert Syst.
, vol.31
, pp. 411-420
-
-
Stahl, F.1
Bramer, M.2
-
76
-
-
84959327515
-
Opening the black box: Revealing interpretable sequence motifs in kernel-based learning algorithms
-
ed. A Appice, PP Rodrigues, VS Costa, J Gama, A Jorge, C Soares Cham, Switz.: Springer
-
Vidovic MM-C, Görnitz N, Müller K-R, Rätsch G, Kloft M. 2015. Opening the black box: revealing interpretable sequence motifs in kernel-based learning algorithms. In Lecture Notes in Computer Science, Vol. 9285: Machine Learning and Knowledge Discovery in Databases, ed. A Appice, PP Rodrigues, VS Costa, J Gama, A Jorge, C Soares, pp. 137-53. Cham, Switz.: Springer
-
(2015)
Lecture Notes in Computer Science: Machine Learning and Knowledge Discovery in Databases
, vol.9285
, pp. 137-153
-
-
Vidovic, M.M.-C.1
Görnitz, N.2
Müller, K.-R.3
Rätsch, G.4
Kloft, M.5
-
78
-
-
84921714097
-
Empowering personalized medicine with big data and semantic web technology: Promises challenges, and use cases
-
Panahiazar M, Taslimitehrani V, Jadhav A, Pathak J. 2014. Empowering personalized medicine with big data and semantic web technology: promises, challenges, and use cases. Proc. Big Data, 2014 IEEE Int. Conf., pp. 790-95
-
(2014)
Proc. Big Data, 2014 IEEE Int. Conf.
, pp. 790-795
-
-
Panahiazar, M.1
Taslimitehrani, V.2
Jadhav, A.3
Pathak, J.4
-
79
-
-
70449404671
-
BioGateway: A semantic systems biology tool for the life sciences
-
Antezana E, BlondeW, Egana M, Rutherford A, Stevens R, et al. 2009. BioGateway: a semantic systems biology tool for the life sciences. BMC Bioinform. 10(Suppl. 10):S11
-
(2009)
BMC Bioinform.
, vol.10
, pp. S11
-
-
Antezana, E.1
Blonde, W.2
Egana, M.3
Rutherford, A.4
Stevens, R.5
-
80
-
-
84920036142
-
Semantic Web repositories for genomics data using the eXframe platform
-
Merrill E, Corlosquet S, Ciccarese P, Clark T, Das S. 2014. Semantic Web repositories for genomics data using the eXframe platform. J. Biomed. Semantics 5:1
-
(2014)
J. Biomed. Semantics
, vol.5
, pp. 1
-
-
Merrill, E.1
Corlosquet, S.2
Ciccarese, P.3
Clark, T.4
Das, S.5
-
81
-
-
84885017699
-
Bio2RDF release 2: Improved coverage, interoperability and provenance of life science linked data
-
ed. P Cimiano, O Corcho, V Presutti, L Hollink, S Rudolph Cham, Switz.: Springer
-
Callahan A, Cruz-Toledo J, Ansell P, Dumontier M. 2013. Bio2RDF release 2: improved coverage, interoperability and provenance of life science linked data. In Lecture Notes in Computer Science, Vol. 7882: The Semantic Web: Semantics and Big Data. ed. P Cimiano, O Corcho, V Presutti, L Hollink, S Rudolph, pp. 200-12. Cham, Switz.: Springer
-
(2013)
Lecture Notes in Computer Science: The Semantic Web: Semantics and Big Data
, vol.7882
, pp. 200-212
-
-
Callahan, A.1
Cruz-Toledo, J.2
Ansell, P.3
Dumontier, M.4
-
82
-
-
84876467333
-
The comparative toxicogenomics database: Update 2013
-
Davis AP, Murphy CG, Johnson R, Lay JM, Lennon-Hopkins K, et al. 2013. The Comparative Toxicogenomics Database: update 2013. Nucleic Acids Res. 41:D1104-14
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D1104-D1114
-
-
Davis, A.P.1
Murphy, C.G.2
Johnson, R.3
Lay, J.M.4
Lennon-Hopkins, K.5
-
83
-
-
38549151817
-
DrugBank: A knowledgebase for drugs, drug actions and drug targets
-
Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, et al. 2008. DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res. 36:D901-6
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. D901-D906
-
-
Wishart, D.S.1
Knox, C.2
Guo, A.C.3
Cheng, D.4
Shrivastava, S.5
-
84
-
-
13444266370
-
OnlineMendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
-
Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. 2005. OnlineMendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 33:D514-17
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. D514-D517
-
-
Hamosh, A.1
Scott, A.F.2
Amberger, J.S.3
Bocchini, C.A.4
McKusick, V.A.5
-
85
-
-
27744460659
-
PharmGKB: The pharmacogenetics and pharmacogenomics knowledge base
-
Thorn CF, Klein TE, Altman RB. 2005. PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base. Methods Mol. Biol. 311:179-91
-
(2005)
Methods Mol. Biol.
, vol.311
, pp. 179-191
-
-
Thorn, C.F.1
Klein, T.E.2
Altman, R.B.3
-
86
-
-
77954592817
-
ResearchEHR: Use of semantic web technologies and archetypes for the description of EHRs
-
Robles M, Fernández-Breis JT, Maldonado JA, Moner D, Martnez-Costa C, et al. 2010. ResearchEHR: use of semantic web technologies and archetypes for the description of EHRs. Stud.Health Technol. Inform. 155:129
-
(2010)
Stud.Health Technol. Inform.
, vol.155
, pp. 129
-
-
Robles, M.1
Fernández-Breis, J.T.2
Maldonado, J.A.3
Moner, D.4
Martnez-Costa, C.5
-
87
-
-
83255163226
-
Toward semantic web based knowledge representation and extraction from electronic health records
-
Tao C, Pathak J, Welch SR, Bouamrane M-M, Huff SM, Chute CG. 2011. Toward semantic web based knowledge representation and extraction from electronic health records. Proc. Int. Workshop Manag. Interoperability Complex. Health Syst., pp. 75-78
-
(2011)
Proc. Int. Workshop Manag. Interoperability Complex. Health Syst.
, pp. 75-78
-
-
Tao, C.1
Pathak, J.2
Welch, S.R.3
Bouamrane, M.-M.4
Huff, S.M.5
Chute, C.G.6
-
88
-
-
85052026525
-
OWLing clinical data repositories with the ontology web language
-
Lozano-Rub R, Pastor X, Lozano E. 2014. OWLing clinical data repositories with the ontology web language. JMIR Med. Inform. 2:e14
-
(2014)
JMIR Med. Inform.
, vol.2
, pp. e14
-
-
Lozano-Rub, R.1
Pastor, X.2
Lozano, E.3
-
89
-
-
84889676637
-
Applying semantic web technologies for phenomewide scan using an electronic health record linked Biobank
-
Pathak J, Kiefer RC, Bielinski SJ, Chute CG. 2012. Applying semantic web technologies for phenomewide scan using an electronic health record linked Biobank. J. Biomed. Semantics 3:10
-
(2012)
J. Biomed. Semantics
, vol.3
, pp. 10
-
-
Pathak, J.1
Kiefer, R.C.2
Bielinski, S.J.3
Chute, C.G.4
-
90
-
-
84906242912
-
HDL and cardiovascular disease
-
Rader DJ, Hovingh GK. 2014. HDL and cardiovascular disease. Lancet 384:618-25
-
(2014)
Lancet
, vol.384
, pp. 618-625
-
-
Rader, D.J.1
Hovingh, G.K.2
|