-
1
-
-
84874253819
-
Gene Ontology annotations and resources
-
Consortium, G. O. Gene Ontology annotations and resources. Nucleic acids research 41, D530-D535 (2013).
-
(2013)
Nucleic Acids Research
, vol.41
, pp. D530-D535
-
-
-
2
-
-
75549090213
-
KEGG for representation and analysis of molecular networks involving diseases and drugs
-
Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M. & Hirakawa, M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic acids research 38, D355-D360 (2010).
-
(2010)
Nucleic Acids Research
, vol.38
, pp. D355-D360
-
-
Kanehisa, M.1
Goto, S.2
Furumichi, M.3
Tanabe, M.4
Hirakawa, M.5
-
4
-
-
84891753483
-
The Reactome pathway knowledgebase
-
Croft, D. et al. The Reactome pathway knowledgebase. Nucleic acids research 42, D472-D477 (2014).
-
(2014)
Nucleic Acids Research
, vol.42
, pp. D472-D477
-
-
Croft, D.1
-
5
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America 102, 15545-15550, doi: 10.1073/pnas.0506580102 (2005).
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
-
6
-
-
61449172037
-
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
-
Huang da, W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature protocols 4, 44-57, doi: 10.1038/nprot.2008.211 (2009).
-
(2009)
Nature Protocols
, vol.4
, pp. 44-57
-
-
Da, W.H.1
Sherman, B.T.2
Lempicki, R.A.3
-
7
-
-
24044440971
-
A Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks
-
Maere, S., Heymans, K. & Kuiper, M. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21, 3448-3449, doi: 10.1093/bioinformatics/bti551(2005).
-
(2005)
Bioinformatics
, vol.21
, pp. 3448-3449
-
-
Maere, S.1
Heymans, K.2
Kuiper, M.B.3
-
8
-
-
48449104617
-
GOEAST: A web-based software toolkit for Gene Ontology enrichment analysis
-
Zheng, Q. & Wang, X. J. GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res 36, W358-363, doi: 10.1093/nar/gkn276(2008).
-
(2008)
Nucleic Acids Res
, vol.36
, pp. W358-W363
-
-
Zheng, Q.1
Wang, X.J.2
-
9
-
-
77954269901
-
The GeneMANIA prediction server: Biological network integration for gene prioritization and predicting gene function
-
Warde-Farley, D. et al. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic acids research 38, W214-W220(2010).
-
(2010)
Nucleic Acids Research
, vol.38
, pp. W214-W220
-
-
Warde-Farley, D.1
-
10
-
-
84883575046
-
GeneMANIA prediction server 2013 update
-
Zuberi, K. et al. GeneMANIA prediction server 2013 update. Nucleic acids research 41, W115-W122(2013).
-
(2013)
Nucleic Acids Research
, vol.41
, pp. W115-W122
-
-
Zuberi, K.1
-
11
-
-
34548400259
-
A systems biology approach for pathway level analysis
-
Draghici, S. et al. A systems biology approach for pathway level analysis. Genome Res. 17, 1537-1545 (2007).
-
(2007)
Genome Res.
, vol.17
, pp. 1537-1545
-
-
Draghici, S.1
-
13
-
-
84875981570
-
SPIA: Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway overrepresentation and unusual signaling perturbations
-
Tarca, A. L., Kathri, P. & Draghici, S. SPIA: Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway overrepresentation and unusual signaling perturbations. R projectAvailable: http://bioinformatics.oxfordjournals.org/cgi/reprint/btn577v1 (2011).
-
(2011)
R Project
-
-
Tarca, A.L.1
Kathri, P.2
Draghici, S.3
-
14
-
-
84874720474
-
CePa: An R package for finding significant pathways weighted by multiple network centralities
-
Gu, Z. & Wang, J. CePa: an R package for finding significant pathways weighted by multiple network centralities. Bioinformatics, btt008 (2013).
-
(2013)
Bioinformatics
, pp. btt008
-
-
Gu, Z.1
Wang, J.2
-
15
-
-
84893009656
-
Methods and approaches in the topology-based analysis of biological pathways
-
Mitrea, C. et al. Methods and approaches in the topology-based analysis of biological pathways. Frontiers in physiology 4 (2013).
-
(2013)
Frontiers in Physiology
, vol.4
-
-
Mitrea, C.1
-
16
-
-
80052215666
-
NOA: A novel Network Ontology Analysis method
-
Wang, J. et al. NOA: a novel Network Ontology Analysis method. Nucleic Acids Res 39, e87, doi: 10.1093/nar/gkr251 (2011).
-
(2011)
Nucleic Acids Res
, vol.39
, pp. e87
-
-
Wang, J.1
-
17
-
-
84865975684
-
Network enrichment analysis: Extension of gene-set enrichment analysis to gene networks
-
Alexeyenko, A. et al. Network enrichment analysis: extension of gene-set enrichment analysis to gene networks. BMC bioinformatics 13, 226 (2012).
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 226
-
-
Alexeyenko, A.1
-
18
-
-
84866449583
-
EnrichNet: Network-based gene set enrichment analysis
-
Glaab, E., Baudot, A., Krasnogor, N., Schneider, R. & Valencia, A. EnrichNet: network-based gene set enrichment analysis. Bioinformatics 28, i451-i457, doi: 10.1093/bioinformatics/bts389(2012).
-
(2012)
Bioinformatics
, vol.28
, pp. i451-i457
-
-
Glaab, E.1
Baudot, A.2
Krasnogor, N.3
Schneider, R.4
Valencia, A.5
-
19
-
-
84857791962
-
A network-based gene-weighting approach for pathway analysis
-
Fang, Z., Tian, W. & Ji, H. A network-based gene-weighting approach for pathway analysis. Cell research 22, 565-580 (2011).
-
(2011)
Cell Research
, vol.22
, pp. 565-580
-
-
Fang, Z.1
Tian, W.2
Ji, H.3
-
20
-
-
25444472585
-
Pathway level analysis of gene expression using singular value decomposition
-
Tomfohr, J., Lu, J. & Kepler, T. B. Pathway level analysis of gene expression using singular value decomposition. BMC Bioinformatics 6, 225, doi: 10.1186/1471-2105-6-225(2005).
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 225
-
-
Tomfohr, J.1
Lu, J.2
Kepler, T.B.3
-
21
-
-
84872256757
-
Machine learning and its applications to biology
-
Tarca, A. L., Carey, V. J., Chen, X. W., Romero, R. & Draghici, S. Machine learning and its applications to biology. PLoS Comput Biol 3 (2007).
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Tarca, A.L.1
Carey, V.J.2
Chen, X.W.3
Romero, R.4
Draghici, S.5
-
22
-
-
0345832338
-
A global test for groups of genes: Testing association with a clinical outcome
-
Goeman, J. J., Van De Geer, S. A., De Kort, F. & Van Houwelingen, H. C. A global test for groups of genes: testing association with a clinical outcome. Bioinformatics 20, 93-99, doi: 10.1093/bioinformatics/btg382(2003).
-
(2003)
Bioinformatics
, vol.20
, pp. 93-99
-
-
Goeman, J.J.1
Van De Geer, S.A.2
De Kort, F.3
Van Houwelingen, H.C.4
-
23
-
-
84862275365
-
Down-weighting overlapping genes improves gene set analysis
-
Tarca, A. L., Draghici, S., Bhatti, G. & Romero, R. Down-weighting overlapping genes improves gene set analysis. BMC Bioinformatics13 (2012).
-
(2012)
BMC Bioinformatics
, vol.13
-
-
Tarca, A.L.1
Draghici, S.2
Bhatti, G.3
Romero, R.4
-
24
-
-
51249106466
-
Integrative analysis of RUNX1 downstream pathways and target genes
-
Michaud, J. et al. Integrative analysis of RUNX1 downstream pathways and target genes. BMC genomics 9, 363, doi: 10.1186/1471-2164-9-363 (2008).
-
(2008)
BMC Genomics
, vol.9
, Issue.363
-
-
Michaud, J.1
-
25
-
-
35348890683
-
On testing the significance of sets of genes
-
Efron, B. & Tibshirani, R. On testing the significance of sets of genes. The Annals of Applied Statistics 1, 107-129, doi: 10.1214/07-aoas101(2007).
-
(2007)
The Annals of Applied Statistics
, vol.1
, pp. 107-129
-
-
Efron, B.1
Tibshirani, R.2
-
26
-
-
84896716464
-
A comparison of gene set analysis methods in terms of sensitivity, prioritization and specificity
-
Tarca, A. L., Bhatti, G. & Romero, R. A comparison of gene set analysis methods in terms of sensitivity, prioritization and specificity. PloS one 8, e79217, doi: 10.1371/journal.pone.0079217(2013).
-
(2013)
PloS One
, vol.8
-
-
Tarca, A.L.1
Bhatti, G.2
Romero, R.3
-
27
-
-
35348957264
-
Efficient behavior of small-world networks
-
Latora, V. & Marchiori, M. Efficient behavior of small-world networks. Physical review letters 87, 198701(2001).
-
(2001)
Physical Review Letters
, vol.87
, pp. 198701
-
-
Latora, V.1
Marchiori, M.2
-
28
-
-
66349108078
-
Fewer permutations, more accurate P-values
-
Knijnenburg, T. A., Wessels, L. F., Reinders, M. J. & Shmulevich, I. Fewer permutations, more accurate P-values. Bioinformatics 25, i161-i168(2009).
-
(2009)
Bioinformatics
, vol.25
, pp. i161-i168
-
-
Knijnenburg, T.A.1
Wessels, L.F.2
Reinders, M.J.3
Shmulevich, I.4
-
29
-
-
33645762226
-
A sharper Bonferroni procedure for multiple tests of significance
-
Hochberg, Y. A sharper Bonferroni procedure for multiple tests of significance. Biometrika 75, 800-802(1988).
-
(1988)
Biometrika
, vol.75
, pp. 800-802
-
-
Hochberg, Y.1
-
30
-
-
33749238682
-
Beyond Bonferroni: Less conservative analyses for conservation genetics
-
Narum, S. R. Beyond Bonferroni: Less conservative analyses for conservation genetics. Conservation Genetics 7, 783-787, doi: 10.1007/s10592-005-9056-y(2006).
-
(2006)
Conservation Genetics
, vol.7
, pp. 783-787
-
-
Narum, S.R.1
-
31
-
-
84862185886
-
Comparative interactomics with Funcoup 2.0
-
Alexeyenko, A. et al. Comparative interactomics with Funcoup 2.0. Nucleic Acids Res 40, D821-828, doi: 10.1093/nar/gkr1062(2012).
-
(2012)
Nucleic Acids Res
, vol.40
, pp. D821-D828
-
-
Alexeyenko, A.1
-
32
-
-
84884695491
-
Limited Agreement of Independent RNAi Screens for Virus-Required Host Genes Owes More to False-Negative than False-Positive Factors
-
Hao, L. et al. Limited Agreement of Independent RNAi Screens for Virus-Required Host Genes Owes More to False-Negative than False-Positive Factors. Plos Computational Biology 9, doi: 10.1371/journal.pcbi.1003235(2013).
-
(2013)
Plos Computational Biology
, vol.9
-
-
Hao, L.1
-
33
-
-
76749090540
-
Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication
-
Karlas, A. et al. Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication. Nature 463, 818-822(2010).
-
(2010)
Nature
, vol.463
, pp. 818-822
-
-
Karlas, A.1
-
34
-
-
49649127852
-
Drosophila RNAi screen identifies host genes important for influenza virus replication
-
Hao, L. et al. Drosophila RNAi screen identifies host genes important for influenza virus replication. Nature 454, 890-893(2008).
-
(2008)
Nature
, vol.454
, pp. 890-893
-
-
Hao, L.1
-
35
-
-
72549116887
-
The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus
-
Brass, A. L. et al. The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. Cell 139, 1243-1254(2009).
-
(2009)
Cell
, vol.139
, pp. 1243-1254
-
-
Brass, A.L.1
-
36
-
-
76749108989
-
Human host factors required for influenza virus replication
-
König, R. et al. Human host factors required for influenza virus replication. Nature 463, 813-817(2009).
-
(2009)
Nature
, vol.463
, pp. 813-817
-
-
König, R.1
-
37
-
-
0034069495
-
Gene Ontology: Tool for the unification of biology
-
Ashburner, M. et al. Gene Ontology: tool for the unification of biology. Nature genetics 25, 25-29(2000).
-
(2000)
Nature Genetics
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
-
38
-
-
43349094507
-
The igraph software package for complex network research
-
Csardi, G. & Nepusz, T. The igraph software package for complex network research. InterJournal, Complex Systems 1695 (2006).
-
(2006)
InterJournal, Complex Systems
, vol.1695
-
-
Csardi, G.1
Nepusz, T.2
-
39
-
-
84891796667
-
YeastNet v3: A public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae
-
Kim, H. et al. YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. Nucleic acids research 42, D731-D736 (2014).
-
(2014)
Nucleic Acids Research
, vol.42
, pp. D731-D736
-
-
Kim, H.1
-
40
-
-
78651324347
-
The STRING database in 2011: Functional interaction networks of proteins, globally integrated and scored
-
Szklarczyk, D. et al. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic acids research 39, D561-D568 (2011).
-
(2011)
Nucleic Acids Research
, vol.39
, pp. D561-D568
-
-
Szklarczyk, D.1
-
41
-
-
84876515907
-
STRING v9. 1: Protein-protein interaction networks, with increased coverage and integration
-
Franceschini, A. et al. STRING v9. 1: protein-protein interaction networks, with increased coverage and integration. Nucleic acids research 41, D808-D815(2013).
-
(2013)
Nucleic Acids Research
, vol.41
, pp. D808-D815
-
-
Franceschini, A.1
-
42
-
-
79959898376
-
Prioritizing candidate disease genes by network-based boosting of genome-wide association data
-
Lee, I., Blom, U. M., Wang, P. I., Shim, J. E. & Marcotte, E. M. Prioritizing candidate disease genes by network-based boosting of genome-wide association data. Genome research 21, 1109-1121(2011).
-
(2011)
Genome Research
, vol.21
, pp. 1109-1121
-
-
Lee, I.1
Blom, U.M.2
Wang, P.I.3
Shim, J.E.4
Marcotte, E.M.5
-
43
-
-
4544341015
-
Linear models and empirical Bayes methods for assessing dierential expression in microarray experiments
-
Smyth, G. K. Linear models and empirical Bayes methods for assessing dierential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 3, 3(2004).
-
(2004)
Statistical Applications in Genetics and Molecular Biology
, vol.3
, pp. 3
-
-
Smyth, G.K.1
-
45
-
-
23144455923
-
Recent additions and improvements to the Onto-Tools
-
Khatri, P. et al. Recent additions and improvements to the Onto-Tools. Nucleic Acids Res 33, 762-765(2005).
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 762-765
-
-
Khatri, P.1
-
46
-
-
34547571929
-
Onto-Tools: New additions and improvements in 2006
-
Khatri, P. et al. Onto-Tools: new additions and improvements in 2006. Nucleic Acids Res. 37, 206-211(2007).
-
(2007)
Nucleic Acids Res.
, vol.37
, pp. 206-211
-
-
Khatri, P.1
-
47
-
-
84873608183
-
-
IEEE, Boca Raton, FL
-
Voichita, C., Donato, M. & Draghici, S. in Machine Learning and Applications (ICMLA) 2012 11th International Conference Vol. 1 126-131 (IEEE, Boca Raton, FL, 2012).
-
Machine Learning and Applications (ICMLA) 2012 11th International Conference
, vol.1
, Issue.126-131
, pp. 2012
-
-
Voichita, C.1
Donato, M.2
Draghici S.In3
-
48
-
-
58049215467
-
A novel signaling pathway impact analysis (SPIA)
-
Tarca, A. L. et al. A novel signaling pathway impact analysis (SPIA). Bioinformatics 25, 75-82 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 75-82
-
-
Tarca, A.L.1
-
49
-
-
84861804088
-
Centrality-based pathway enrichment: A systematic approach for finding significant pathways dominated by key genes
-
Gu, Z., Liu, J., Cao, K., Zhang, J. & Wang, J. Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes. BMC Syst. Biol. 6 (2012).
-
(2012)
BMC Syst. Biol.
, vol.6
-
-
Gu, Z.1
Liu, J.2
Cao, K.3
Zhang, J.4
Wang, J.5
-
52
-
-
84856944883
-
An iterative network partition algorithm for accurate identification of dense network modules
-
Sun, S., Dong, X., Fu, Y. & Tian, W. An iterative network partition algorithm for accurate identification of dense network modules. Nucleic Acids Research 40, doi: 10.1093/nar/gkr1103(2012).
-
(2012)
Nucleic Acids Research
, vol.40
-
-
Sun, S.1
Dong, X.2
Fu, Y.3
Tian, W.4
-
53
-
-
84912144889
-
Synaptic, transcriptional and chromatin genes disrupted in autism
-
De Rubeis, S. et al. Synaptic, transcriptional and chromatin genes disrupted in autism. Nature 515, 209-215, doi: 10.1038/nature13772(2014).
-
(2014)
Nature
, vol.515
, pp. 209-215
-
-
De Rubeis, S.1
-
54
-
-
84912101541
-
The contribution of de novo coding mutations to autism spectrum disorder
-
Iossifov, I., O'Roak, B. J. & Sanders, S. J. The contribution of de novo coding mutations to autism spectrum disorder. Nature(2014).
-
(2014)
Nature
-
-
Iossifov, I.1
O'Roak, B.J.2
Sanders, S.J.3
-
55
-
-
4644326931
-
Genomic analysis of regulatory network dynamics reveals large topological changes
-
Luscombe, N. M. et al. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431, 308-312(2004).
-
(2004)
Nature
, vol.431
, pp. 308-312
-
-
Luscombe, N.M.1
-
56
-
-
0035754080
-
To cycle or not to cycle: A critical decision in cancer
-
Malumbres, M. & Barbacid, M. To cycle or not to cycle: a critical decision in cancer. Nature Rev. Cancer 1, 222-231(2001).
-
(2001)
Nature Rev. Cancer
, vol.1
, pp. 222-231
-
-
Malumbres, M.1
Barbacid, M.2
-
57
-
-
0025816663
-
Folding of influenza hemagglutinin in the endoplasmic reticulum
-
Braakman, I., Hoover-Litty, H., Wagner, K. R. & Helenius, A. Folding of influenza hemagglutinin in the endoplasmic reticulum. The Journal of cell biology 114, 401-411(1991).
-
(1991)
The Journal of Cell Biology
, vol.114
, pp. 401-411
-
-
Braakman, I.1
Hoover-Litty, H.2
Wagner, K.R.3
Helenius, A.4
-
58
-
-
27144530248
-
Towards a proteome-scale map of the human protein-protein interaction network
-
Rual, J. F. et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437, 1173-1178, doi: 10.1038/nature04209(2005).
-
(2005)
Nature
, vol.437
, pp. 1173-1178
-
-
Rual, J.F.1
-
59
-
-
84859910819
-
Vitamin D and autism: Clinical review
-
Kocovska, E., Fernell, E., Billstedt, E., Minnis, H. & Gillberg, C. Vitamin D and autism: Clinical review. Research in Developmental Disabilities 33, 1541-1550, doi: 10.1016/j.ridd.2012.02.015(2012).
-
(2012)
Research in Developmental Disabilities
, vol.33
, pp. 1541-1550
-
-
Kocovska, E.1
Fernell, E.2
Billstedt, E.3
Minnis, H.4
Gillberg, C.5
-
60
-
-
0035317648
-
Suppressed GABAergic inhibition as a common factor in suspected etiologies of autism
-
Hussman, J. P. Suppressed GABAergic inhibition as a common factor in suspected etiologies of autism. Journal of Autism and Developmental Disorders 31, 247-248, doi: 10.1023/a:1010715619091(2001).
-
(2001)
Journal of Autism and Developmental Disorders
, vol.31
, pp. 247-248
-
-
Hussman, J.P.1
-
61
-
-
0027395939
-
Identification of functionally related genes that stimulate early meiotic gene expression in yeast
-
Su, S. & Mitchell, A. P. Identification of functionally related genes that stimulate early meiotic gene expression in yeast. Genetics 133, 67-77(1993).
-
(1993)
Genetics
, vol.133
, pp. 67-77
-
-
Su, S.1
Mitchell, A.P.2
-
62
-
-
0031772260
-
Global regulatory functions of Oaf1p and Pip2p (Oaf2p), transcription factors that regulate genes encoding peroxisomal proteins in Saccharomyces cerevisiae
-
Karpichev, I. V. & Small, G. M. Global regulatory functions of Oaf1p and Pip2p (Oaf2p), transcription factors that regulate genes encoding peroxisomal proteins in Saccharomyces cerevisiae. Molecular and cellular biology 18, 6560-6570(1998).
-
(1998)
Molecular and Cellular Biology
, vol.18
, pp. 6560-6570
-
-
Karpichev, I.V.1
Small, G.M.2
-
63
-
-
18344377030
-
The p53 pathway: Positive and negative feedback loops
-
Harris, S. L. & Levine, A. J. The p53 pathway: positive and negative feedback loops. Oncogene 24, 2899-2908, doi: 10.1038/sj.onc.1208615 (2005).
-
(2005)
Oncogene
, vol.24
, pp. 2899-2908
-
-
Harris, S.L.1
Levine, A.J.2
-
65
-
-
77954376945
-
GOing Bayesian: Model-based gene set analysis of genome-scale data
-
Bauer, S., Gagneur, J. & Robinson, P. N. GOing Bayesian: model-based gene set analysis of genome-scale data. Nucleic acids research 38, 3523-3532(2010).
-
(2010)
Nucleic Acids Research
, vol.38
, pp. 3523-3532
-
-
Bauer, S.1
Gagneur, J.2
Robinson, P.N.3
|