-
1
-
-
69549110058
-
Knowledge based identification of essential signaling from genome-scale siRNA experiments
-
Bankhead,A. et al. (2009) Knowledge based identification of essential signaling from genome-scale siRNA experiments. BMC Syst. Biol., 3, 80.
-
(2009)
BMC Syst. Biol.
, vol.3
, pp. 80
-
-
Bankhead, A.1
-
2
-
-
78149489180
-
RNA interference (RNAi) screening approach identifies agents that enhance paclitaxel activity in breast cancer cells
-
Bauer,J.A. et al. (2010) RNA interference (RNAi) screening approach identifies agents that enhance paclitaxel activity in breast cancer cells. Breast Cancer Res., 12, R41.
-
(2010)
Breast Cancer Res.
, vol.12
-
-
Bauer, J.A.1
-
3
-
-
12144289681
-
A large-scale RNAi screen in human cells identifies new components of the p53 pathway
-
Berns,K. et al. (2004) A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature, 428, 431-437.
-
(2004)
Nature
, vol.428
, pp. 431-437
-
-
Berns, K.1
-
4
-
-
68349112682
-
Statistical methods for analysis of high-throughput RNA interference screens
-
Birmingham,A. et al. (2009) Statistical methods for analysis of high-throughput RNA interference screens. Nat. Methods, 6, 569-575.
-
(2009)
Nat. Methods
, vol.6
, pp. 569-575
-
-
Birmingham, A.1
-
5
-
-
39349097864
-
Identification of host proteins required for HIV infection through a functional genomic screen
-
Brass,A. et al. (2008) Identification of host proteins required for HIV infection through a functional genomic screen. Science, 15, 921-926.
-
(2008)
Science
, vol.15
, pp. 921-926
-
-
Brass, A.1
-
6
-
-
72549116887
-
The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus
-
Brass,A.L. et al. (2009) The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. Cell, 139, 1243-1254.
-
(2009)
Cell
, vol.139
, pp. 1243-1254
-
-
Brass, A.L.1
-
7
-
-
20844450402
-
Differential network expression during drug and stress response
-
Cabusora,L. et al. (2005) Differential network expression during drug and stress response. Bioinformatics, 21, 2898-2905.
-
(2005)
Bioinformatics
, vol.21
, pp. 2898-2905
-
-
Cabusora, L.1
-
8
-
-
78149465975
-
A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity
-
Chia,N.Y. et al. (2010) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Nature, 468, 316-320.
-
(2010)
Nature
, vol.468
, pp. 316-320
-
-
Chia, N.Y.1
-
9
-
-
39049097168
-
Median absolute deviation to improve hit selection for genomescale RNAi screens
-
Chung,N. et al. (2008) Median absolute deviation to improve hit selection for genomescale RNAi screens. J. Biomol. Screen., 13, 149-158.
-
(2008)
J. Biomol. Screen.
, vol.13
, pp. 149-158
-
-
Chung, N.1
-
10
-
-
76249128583
-
Vps4 and the ESCRT-III complex are required for the release of infectious hepatitis C virus particles
-
Corless,L. et al. (2010) Vps4 and the ESCRT-III complex are required for the release of infectious hepatitis C virus particles. J. Gen. Virol., 91, 362-372.
-
(2010)
J. Gen. Virol.
, vol.91
, pp. 362-372
-
-
Corless, L.1
-
11
-
-
34447265020
-
Herpes simplex virus type 1 cytoplasmic envelopment requires functional Vps4
-
Crump,C.M. et al. (2007) Herpes simplex virus type 1 cytoplasmic envelopment requires functional Vps4. J. Virol., 81, 7380-7387.
-
(2007)
J. Virol.
, vol.81
, pp. 7380-7387
-
-
Crump, C.M.1
-
12
-
-
18244400410
-
Functional genomic analysis of the Wnt-wingless signaling pathway
-
DasGupta,R. et al. (2005) Functional genomic analysis of the Wnt-wingless signaling pathway. Science, 308, 826-833.
-
(2005)
Science
, vol.308
, pp. 826-833
-
-
DasGupta, R.1
-
13
-
-
60749090295
-
Gene-set analysis and reduction
-
Dinu,I. et al. (2009) Gene-set analysis and reduction. Brief. Bioinformatics, 10, 24-34.
-
(2009)
Brief. Bioinformatics
, vol.10
, pp. 24-34
-
-
Dinu, I.1
-
14
-
-
46249128543
-
Identifying functional modules in protein-protein interaction networks: an integrated exact approach
-
Dittrich,M.T. et al. (2008) Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics, 24, i223-i231.
-
(2008)
Bioinformatics
, vol.24
-
-
Dittrich, M.T.1
-
15
-
-
33646187810
-
High-throughput RNAi screening in cultured cells: a user's guide
-
Echeverri,C.J. and Perrimon,N. (2006) High-throughput RNAi screening in cultured cells: a user's guide. Nat. Rev. Genet., 7, 373-384.
-
(2006)
Nat. Rev. Genet.
, vol.7
, pp. 373-384
-
-
Echeverri, C.J.1
Perrimon, N.2
-
16
-
-
17944363138
-
Tsg101 and the vacuolar protein sorting pathway are essential for HIV-1 budding
-
Garrus,J.E. et al. (2001) Tsg101 and the vacuolar protein sorting pathway are essential for HIV-1 budding. Cell, 107, 55-65.
-
(2001)
Cell
, vol.107
, pp. 55-65
-
-
Garrus, J.E.1
-
17
-
-
34249663294
-
Analyzing gene expression data in terms of gene sets: methodological issues
-
Goeman,J.J. and Buhlmann,P. (2007) Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics, 23, 980-987.
-
(2007)
Bioinformatics
, vol.23
, pp. 980-987
-
-
Goeman, J.J.1
Buhlmann, P.2
-
18
-
-
80053442100
-
Edge-based scoring and searching method for identifying conditionresponsive protein-protein interaction sub-network
-
Guo,Z. et al. (2007) Edge-based scoring and searching method for identifying conditionresponsive protein-protein interaction sub-network. Bioinformatics, 63, 3912-3918.
-
(2007)
Bioinformatics
, vol.63
, pp. 3912-3918
-
-
Guo, Z.1
-
19
-
-
0038014879
-
Co-clustering of biological networks and gene expression data
-
Hanisch,D. et al. (2002) Co-clustering of biological networks and gene expression data. Bioinformatics, 18 (Suppl. 1), S145-S154.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Hanisch, D.1
-
20
-
-
0033518234
-
From molceular to modular cell biology
-
Hartwell,L.H. et al. (1999) From molceular to modular cell biology. Nature, 402, C47-C52.
-
(1999)
Nature
, vol.402
-
-
Hartwell, L.H.1
-
21
-
-
64349096829
-
Agenome-wide RNAi screen identifies a new transcriptional module required for self-renewal
-
Hu,G. et al. (2009)Agenome-wide RNAi screen identifies a new transcriptional module required for self-renewal. Genes Dev., 23, 837-848.
-
(2009)
Genes Dev.
, vol.23
, pp. 837-848
-
-
Hu, G.1
-
22
-
-
0000801240
-
Discovering regulatory and signalling circuits in molecular interaction networks
-
Ideker,T. et al. (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics, 18, S233-S240.
-
(2002)
Bioinformatics
, vol.18
-
-
Ideker, T.1
-
23
-
-
58149193234
-
STRING 8-a global view on proteins and their functional interactions in 630 organisms
-
Jensen,L.J. et al. (2009) STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res., 37, D412-D416.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Jensen, L.J.1
-
24
-
-
78049437880
-
Use of data-biased random walks on graphs for the retrieval of context-specific networks from genomic data
-
Komurov,K. et al. (2010) Use of data-biased random walks on graphs for the retrieval of context-specific networks from genomic data. PLoS Comput. Biol., 6, e1000889.
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
Komurov, K.1
-
25
-
-
35848929692
-
Aprobability-based approach for the analysis of large-scale RNAi screens
-
König,R. et al. (2007)Aprobability-based approach for the analysis of large-scale RNAi screens. Nat. Methods, 4, 847-849.
-
(2007)
Nat. Methods
, vol.4
, pp. 847-849
-
-
König, R.1
-
26
-
-
34548157926
-
Hepatitis B virus maturation is sensitive to functional inhibition of ESCRT-III, Vps4, and gamma 2-adaptin
-
Lambert,C. et al. (2007) Hepatitis B virus maturation is sensitive to functional inhibition of ESCRT-III, Vps4, and gamma 2-adaptin. J. Virol., 81, 9050-9060.
-
(2007)
J. Virol.
, vol.81
, pp. 9050-9060
-
-
Lambert, C.1
-
27
-
-
70349513508
-
A genome-wide genetic screen for host factors required for hepatitis C virus propagation
-
Li,Q. et al. (2009) A genome-wide genetic screen for host factors required for hepatitis C virus propagation. Proc. Natl Acad. Sci. USA, 106, 16410-16415.
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 16410-16415
-
-
Li, Q.1
-
28
-
-
38949165049
-
Comparative evaluation of gene-set analysis methods
-
Liu,Q. et al. (2007) Comparative evaluation of gene-set analysis methods. BMC Bioinformatics, 8, 431.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 431
-
-
Liu, Q.1
-
29
-
-
32344448950
-
Statistical practice in high-throughput screening data analysis
-
Malo,N. et al. (2006) Statistical practice in high-throughput screening data analysis. Nat. Biotechnol., 24, 167-175.
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 167-175
-
-
Malo, N.1
-
30
-
-
0035658023
-
HIV-1 and Ebola virus encode small peptide motifs that recruit Tsg101 to sites of particle assembly to facilitate egress
-
Martin-Serrano,J. et al. (2001) HIV-1 and Ebola virus encode small peptide motifs that recruit Tsg101 to sites of particle assembly to facilitate egress. Nat. Med., 7, 1313-1319.
-
(2001)
Nat. Med.
, vol.7
, pp. 1313-1319
-
-
Martin-Serrano, J.1
-
31
-
-
77956482678
-
Gene set analysis exploiting the topology of a pathway
-
Massa,M.S. et al. (2010) Gene set analysis exploiting the topology of a pathway. BMC Syst. Biol., 4, 121.
-
(2010)
BMC Syst. Biol.
, vol.4
, pp. 121
-
-
Massa, M.S.1
-
32
-
-
34248593385
-
Gene expression network analysis and applications to immunology
-
Nacu,S. et al. (2007) Gene expression network analysis and applications to immunology. Bioinformatics, 23, 850-858.
-
(2007)
Bioinformatics
, vol.23
, pp. 850-858
-
-
Nacu, S.1
-
33
-
-
15944402798
-
Inferring pathways from gene lists using a literature-derived network of biological relationships
-
Rajagopalan,D. and Agarwal,P. (2005) Inferring pathways from gene lists using a literature-derived network of biological relationships. Bioinformatics, 21, 788-793.
-
(2005)
Bioinformatics
, vol.21
, pp. 788-793
-
-
Rajagopalan, D.1
Agarwal, P.2
-
34
-
-
38449105972
-
Hepatitis C virus infection: a current review
-
Senecal,D.L. and Morelli,J. (2007) Hepatitis C virus infection: a current review. JAAPA, 20, 21-25.
-
(2007)
JAAPA
, vol.20
, pp. 21-25
-
-
Senecal, D.L.1
Morelli, J.2
-
35
-
-
34047202181
-
Deciphering protein-protein interactions. Part I. Experimental techniques and databases
-
Shoemaker,B.A. and Panchenko,A.R. (2007) Deciphering protein-protein interactions. Part I. Experimental techniques and databases. PLoS Comput. Biol., 3, e42.
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Shoemaker, B.A.1
Panchenko, A.R.2
-
36
-
-
3142706495
-
New methods for joint analysis of biological networks and expression data
-
Sohler,F. et al. (2004) New methods for joint analysis of biological networks and expression data. Bioinformatics, 20, 1517-1521.
-
(2004)
Bioinformatics
, vol.20
, pp. 1517-1521
-
-
Sohler, F.1
-
37
-
-
0036020892
-
A direct approach to false discovery rates
-
Storey,J.D. (2002) A direct approach to false discovery rates. J. R. Stat. Soc., 64, 479--498.
-
(2002)
J. R. Stat. Soc.
, vol.64
, pp. 479-498
-
-
Storey, J.D.1
-
38
-
-
61849160363
-
Afunctional genomic screen identifies cellular cofactors of hepatitis C virus replication
-
Tai,A. et al. (2009)Afunctional genomic screen identifies cellular cofactors of hepatitis C virus replication. Cell Host Microbe, 5, 298-307.
-
(2009)
Cell Host Microbe
, vol.5
, pp. 298-307
-
-
Tai, A.1
-
39
-
-
58049215467
-
Anovel signaling pathway impact analysis
-
Tarca,A.L. et al. (2009)Anovel signaling pathway impact analysis. Bioinformatics, 25, 75-82.
-
(2009)
Bioinformatics
, vol.25
, pp. 75-82
-
-
Tarca, A.L.1
-
40
-
-
34548742517
-
Identification of functional modules using network topology and high-throughput data
-
Ulitsky,I. and Shamir,R. (2007) Identification of functional modules using network topology and high-throughput data. BMC Syst. Biol., 1, 8.
-
(2007)
BMC Syst. Biol.
, vol.1
, pp. 8
-
-
Ulitsky, I.1
Shamir, R.2
-
41
-
-
0035830505
-
A biological atlas of functional maps
-
Vidal,M. (2001) A biological atlas of functional maps. Cell, 104, 333-339.
-
(2001)
Cell
, vol.104
, pp. 333-339
-
-
Vidal, M.1
-
42
-
-
67649124461
-
A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila
-
Wang,L. et al. (2009) A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila. BMC Genomics, 10, 220.
-
(2009)
BMC Genomics
, vol.10
, pp. 220
-
-
Wang, L.1
-
43
-
-
51249111048
-
An analysis of normalization methods for Drosophila RNAi genomic screens and development of a robust validation scheme
-
Wiles,A.M. et al. (2008) An analysis of normalization methods for Drosophila RNAi genomic screens and development of a robust validation scheme. J. Biomol. Screen., 13, 777-784.
-
(2008)
J. Biomol. Screen.
, vol.13
, pp. 777-784
-
-
Wiles, A.M.1
-
44
-
-
73049104551
-
An RNAi screen identifies TRRAP as a regulator of brain tumor-initiating cell differentiation
-
Wurdak,H. et al. (2010) An RNAi screen identifies TRRAP as a regulator of brain tumor-initiating cell differentiation. Cell Stem Cell, 6, 37-47.
-
(2010)
Cell Stem Cell
, vol.6
, pp. 37-47
-
-
Wurdak, H.1
-
45
-
-
56349121125
-
An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer
-
Zender,L. et al. (2008) An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer. Cell, 135, 852-864.
-
(2008)
Cell
, vol.135
, pp. 852-864
-
-
Zender, L.1
-
46
-
-
0033003760
-
A simple statistical parameter for use in evaluation and validation of high throughput screening assays
-
Zhang,J.H. et al. (1999) A simple statistical parameter for use in evaluation and validation of high throughput screening assays. J. Biomol. Screen., 4, 67-73.
-
(1999)
J. Biomol. Screen.
, vol.4
, pp. 67-73
-
-
Zhang, J.H.1
-
47
-
-
34547809341
-
A new method with flexible and balanced control of false negatives and false positives for hit selection in RNA interference high-throughput screening assays
-
Zhang,J.H. (2007a) A new method with flexible and balanced control of false negatives and false positives for hit selection in RNA interference high-throughput screening assays. J. Biomol. Screen., 12, 645-655.
-
(2007)
J. Biomol. Screen.
, vol.12
, pp. 645-655
-
-
Zhang, J.H.1
-
48
-
-
33947167826
-
A pair of new statistical parameters for quality control in RNA interference high-throughput screening assays
-
Zhang,J.H. (2007b) A pair of new statistical parameters for quality control in RNA interference high-throughput screening assays. Genomics, 89, 552-561.
-
(2007)
Genomics
, vol.89
, pp. 552-561
-
-
Zhang, J.H.1
-
49
-
-
34547485288
-
A high-throughput siRNA library screen identifies osteogenic suppressors in human mesenchymal stem cells
-
Zhao,Y. and Ding,S. (2007) A high-throughput siRNA library screen identifies osteogenic suppressors in human mesenchymal stem cells. Proc. Natl Acad. Sci. USA, 104, 9673-9678.
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 9673-9678
-
-
Zhao, Y.1
Ding, S.2
-
50
-
-
55249088255
-
Genome-scale RNAi screen for host factors required for HIV replication
-
Zhou,H. et al. (2008) Genome-scale RNAi screen for host factors required for HIV replication. Cell Host Microbe, 4, 495-504.
-
(2008)
Cell Host Microbe
, vol.4
, pp. 495-504
-
-
Zhou, H.1
|