-
1
-
-
22744458472
-
Pathways to the analysis of microarray data
-
Curtis, R. K., Orešič, M., Vidal-Puig, A., Pathways to the analysis of microarray data. Trends Biotechnol. 2005, 23, 429-435.
-
(2005)
Trends Biotechnol.
, vol.23
, pp. 429-435
-
-
Curtis, R.K.1
Orešič, M.2
Vidal-Puig, A.3
-
2
-
-
39149115688
-
Bioinformatics applications for pathway analysis of microarray data
-
Werner, T., Bioinformatics applications for pathway analysis of microarray data. Curr. Opin. Biotechnol. 2008, 19, 50-54.
-
(2008)
Curr. Opin. Biotechnol.
, vol.19
, pp. 50-54
-
-
Werner, T.1
-
3
-
-
84855710474
-
Combining literature text mining with microarray data: advances for system biology modeling
-
bbr018
-
Faro, A., Giordano, D., Spampinato, C., Combining literature text mining with microarray data: advances for system biology modeling. Brief. Bioinform. 2011, bbr018.
-
(2011)
Brief. Bioinform.
-
-
Faro, A.1
Giordano, D.2
Spampinato, C.3
-
4
-
-
0037434977
-
Biomedical informatics for proteomics
-
Boguski, M. S., McIntosh, M. W., Biomedical informatics for proteomics. Nature 2003, 422, 233-237.
-
(2003)
Nature
, vol.422
, pp. 233-237
-
-
Boguski, M.S.1
McIntosh, M.W.2
-
5
-
-
33750600611
-
Proteome informatics I: bioinformatics tools for processing experimental data
-
Palagi, P. M., Hernandez, P., Walther, D., Appel, R. D., Proteome informatics I: bioinformatics tools for processing experimental data. Proteomics 2006, 6, 5435-44.
-
(2006)
Proteomics
, vol.6
, pp. 5435-5444
-
-
Palagi, P.M.1
Hernandez, P.2
Walther, D.3
Appel, R.D.4
-
6
-
-
67349208911
-
Bioinformatics analysis of mass spectrometry-based proteomics data sets
-
Kumar, C., Mann, M., Bioinformatics analysis of mass spectrometry-based proteomics data sets. Febs Lett. 2009, 583, 1703-1712.
-
(2009)
Febs Lett.
, vol.583
, pp. 1703-1712
-
-
Kumar, C.1
Mann, M.2
-
7
-
-
77949732319
-
From proteome lists to biological impact- tools and strategies for the analysis of large MS data sets
-
Malik, R., Dulla, K., Nigg, E. A., Körner, R., From proteome lists to biological impact- tools and strategies for the analysis of large MS data sets. Proteomics 2010, 10, 1270-1283.
-
(2010)
Proteomics
, vol.10
, pp. 1270-1283
-
-
Malik, R.1
Dulla, K.2
Nigg, E.A.3
Körner, R.4
-
8
-
-
79551483264
-
Discussion on common data analysis strategies used in MS-based proteomics
-
Matthiesen, R., Azevedo, L., Amorim, A., Carvalho, A.S., Discussion on common data analysis strategies used in MS-based proteomics. Proteomics 2011, 11, 604-619.
-
(2011)
Proteomics
, vol.11
, pp. 604-619
-
-
Matthiesen, R.1
Azevedo, L.2
Amorim, A.3
Carvalho, A.S.4
-
9
-
-
84896400808
-
Computational proteomics: designing a comprehensive analytical strategy
-
Goh, W. W. B., Wong, L., Computational proteomics: designing a comprehensive analytical strategy. Drug Discov. Today 2014, 19, 266-274.
-
(2014)
Drug Discov. Today
, vol.19
, pp. 266-274
-
-
Goh, W.W.B.1
Wong, L.2
-
10
-
-
33750601225
-
Proteome informatics II: Bioinformatics for comparative proteomics
-
Lisacek, F., Cohen-Boulakia, S., Appel, R. D., Proteome informatics II: Bioinformatics for comparative proteomics. Proteomics 2006, 6, 5445-5466.
-
(2006)
Proteomics
, vol.6
, pp. 5445-5466
-
-
Lisacek, F.1
Cohen-Boulakia, S.2
Appel, R.D.3
-
11
-
-
0037293075
-
Global functional profiling of gene expression
-
Drăghici, S., Khatri, P., Martins, R. P., Ostermeier, G. C., Krawetz, S. A., Global functional profiling of gene expression. Genomics 2003, 81, 98-104.
-
(2003)
Genomics
, vol.81
, pp. 98-104
-
-
Drăghici, S.1
Khatri, P.2
Martins, R.P.3
Ostermeier, G.C.4
Krawetz, S.A.5
-
12
-
-
24644470505
-
Ontological analysis of gene expression data: current tools, limitations, and open problems
-
Khatri, P., Drăghici, S., Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 2005, 21, 3587-3595.
-
(2005)
Bioinformatics
, vol.21
, pp. 3587-3595
-
-
Khatri, P.1
Drăghici, S.2
-
13
-
-
35748978819
-
Fun&Co: identification of key functional differences in transcriptomes
-
Gamberoni, G., Lamma, E., Lodo, G., Marchesini, J. et al., Fun&Co: identification of key functional differences in transcriptomes. Bioinformatics 2007, 23, 2725-2732.
-
(2007)
Bioinformatics
, vol.23
, pp. 2725-2732
-
-
Gamberoni, G.1
Lamma, E.2
Lodo, G.3
Marchesini, J.4
-
14
-
-
34249663294
-
Analyzing gene expression data in terms of gene sets: methodological issues
-
Goeman, J. J., Bühlmann, P., Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics 2007, 23, 980-987.
-
(2007)
Bioinformatics
, vol.23
, pp. 980-987
-
-
Goeman, J.J.1
Bühlmann, P.2
-
15
-
-
48449105128
-
CoPub: a literature-based keyword enrichment tool for microarray data analysis
-
Frijters, R., Heupers, B., Beek, P. van, Bouwhuis, M. et al., CoPub: a literature-based keyword enrichment tool for microarray data analysis. Nucleic Acids Res. 2008, 36, W406-W410.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. W406-W410
-
-
Frijters, R.1
Heupers, B.2
Beek, P.v.3
Bouwhuis, M.4
-
16
-
-
58549112996
-
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
-
Huang, D. W., Sherman, B. T., Lempicki, R. A., Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009, 37, 1-13.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 1-13
-
-
Huang, D.W.1
Sherman, B.T.2
Lempicki, R.A.3
-
17
-
-
79959410946
-
From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems
-
Geistlinger, L., Csaba, G., Küffner, R., Mulder, N., Zimmer, R., From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems. Bioinformatics 2011, 27, i366-i373.
-
(2011)
Bioinformatics
, vol.27
, pp. i366-i373
-
-
Geistlinger, L.1
Csaba, G.2
Küffner, R.3
Mulder, N.4
Zimmer, R.5
-
18
-
-
79956322553
-
Global quantification of mammalian gene expression control
-
Schwanhäusser, B., Busse, D., Li, N., Dittmar, G. et al., Global quantification of mammalian gene expression control. Nature 2011, 473, 337-342.
-
(2011)
Nature
, vol.473
, pp. 337-342
-
-
Schwanhäusser, B.1
Busse, D.2
Li, N.3
Dittmar, G.4
-
19
-
-
84874805815
-
The challenge of the proteome dynamic range and its implications for in-depth proteomics
-
Zubarev, R. A., The challenge of the proteome dynamic range and its implications for in-depth proteomics. Proteomics 2013, 13, 723-726.
-
(2013)
Proteomics
, vol.13
, pp. 723-726
-
-
Zubarev, R.A.1
-
20
-
-
79951747696
-
The necessity of adjusting tests of protein category enrichment in discovery proteomics
-
Louie, B., Higdon, R., Kolker, E., The necessity of adjusting tests of protein category enrichment in discovery proteomics. Bioinformatics 2010, 26, 3007-3011.
-
(2010)
Bioinformatics
, vol.26
, pp. 3007-3011
-
-
Louie, B.1
Higdon, R.2
Kolker, E.3
-
21
-
-
84901599553
-
A draft map of the human proteome
-
Kim, M. S., Pinto, S. M., Getnet, D., Nirujogi, R. 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
-
22
-
-
84901611036
-
Mass-spectrometry-based draft of the human proteome
-
Wilhelm, M., Schlegl, J., Hahne, H., Gholami, A. M. et al., Mass-spectrometry-based draft of the human proteome. Nature 2014, 509, 582-587.
-
(2014)
Nature
, vol.509
, pp. 582-587
-
-
Wilhelm, M.1
Schlegl, J.2
Hahne, H.3
Gholami, A.M.4
-
23
-
-
84896693880
-
Machine learning applications in proteomics research: How the past can boost the future
-
Kelchtermans, P., Bittremieux, W., De Grave, K., Degroeve, S. et al., Machine learning applications in proteomics research: How the past can boost the future. Proteomics 2014, 14, 353-366.
-
(2014)
Proteomics
, vol.14
, pp. 353-366
-
-
Kelchtermans, P.1
Bittremieux, W.2
De Grave, K.3
Degroeve, S.4
-
24
-
-
0036746362
-
Evaluation of proteome reference maps for cross-species identification of proteins by peptide mass fingerprinting
-
Mathesius, U., Imin, N., Chen, H., Djordjevic, M. A. et al., Evaluation of proteome reference maps for cross-species identification of proteins by peptide mass fingerprinting. Proteomics 2002, 2, 1288-1303.
-
(2002)
Proteomics
, vol.2
, pp. 1288-1303
-
-
Mathesius, U.1
Imin, N.2
Chen, H.3
Djordjevic, M.A.4
-
25
-
-
1542720728
-
Construction of a two-dimensional gel electrophoresis protein database for the Nicotiana tabacum cv. Bright Yellow-2 cell suspension culture
-
Laukens, K., Deckers, P., Esmans, E., Van Onckelen, H., Witters, E., Construction of a two-dimensional gel electrophoresis protein database for the Nicotiana tabacum cv. Bright Yellow-2 cell suspension culture. Proteomics 2004, 4, 720-727.
-
(2004)
Proteomics
, vol.4
, pp. 720-727
-
-
Laukens, K.1
Deckers, P.2
Esmans, E.3
Van Onckelen, H.4
Witters, E.5
-
26
-
-
80052033624
-
Protein identification using MS/MS data
-
Cottrell, J. S., Protein identification using MS/MS data. J. Proteomics 2011, 74, 1842-1851.
-
(2011)
J. Proteomics
, vol.74
, pp. 1842-1851
-
-
Cottrell, J.S.1
-
27
-
-
77958549006
-
Large-scale protein interactome mapping: strategies and opportunities
-
Lievens, S., Eyckerman, S., Lemmens, I., Tavernier, J., Large-scale protein interactome mapping: strategies and opportunities. Expert Rev. Proteomics 2010, 7, 679-690.
-
(2010)
Expert Rev. Proteomics
, vol.7
, pp. 679-690
-
-
Lievens, S.1
Eyckerman, S.2
Lemmens, I.3
Tavernier, J.4
-
28
-
-
77955608634
-
Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana
-
Van Leene, J., Hollunder, J., Eeckhout, D., Persiau, G. et al., Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. Mol. Syst. Biol. 2010, 6, 397.
-
(2010)
Mol. Syst. Biol.
, vol.6
, pp. 397
-
-
Van Leene, J.1
Hollunder, J.2
Eeckhout, D.3
Persiau, G.4
-
29
-
-
84898612068
-
Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism
-
Corominas, R., Yang, X., Lin, G. N., Kang, S. et al., Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism. Nat. Commun. 2014, 5, 3650.
-
(2014)
Nat. Commun.
, vol.5
, pp. 3650
-
-
Corominas, R.1
Yang, X.2
Lin, G.N.3
Kang, S.4
-
30
-
-
77955444211
-
Application of chemoproteomics to drug discovery: identification of a clinical candidate targeting Hsp90
-
Fadden, P., Huang, K. H., Veal, J. M., Steed, P. M. et al., Application of chemoproteomics to drug discovery: identification of a clinical candidate targeting Hsp90. Chem. Biol. 2010, 17, 686-694.
-
(2010)
Chem. Biol.
, vol.17
, pp. 686-694
-
-
Fadden, P.1
Huang, K.H.2
Veal, J.M.3
Steed, P.M.4
-
31
-
-
84890641204
-
The coming of age of phosphoproteomics-from large data sets to inference of protein functions
-
Roux, P. P., Thibault, P., The coming of age of phosphoproteomics-from large data sets to inference of protein functions. Mol. Cell. Proteomics 2013, 12, 3453-3464.
-
(2013)
Mol. Cell. Proteomics
, vol.12
, pp. 3453-3464
-
-
Roux, P.P.1
Thibault, P.2
-
32
-
-
84857817395
-
Mass spectrometry-based proteomics strategies for protease cleavage site identification
-
Van den Berg, B. H. J., Tholey, A., Mass spectrometry-based proteomics strategies for protease cleavage site identification. Proteomics 2012, 12, 516-529.
-
(2012)
Proteomics
, vol.12
, pp. 516-529
-
-
Van den Berg, B.H.J.1
Tholey, A.2
-
33
-
-
84865576726
-
Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present
-
Bantscheff, M., Lemeer, S., Savitski, M. M., Kuster, B., Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present. Anal. Bioanal. Chem. 2012, 404, 939-965.
-
(2012)
Anal. Bioanal. Chem.
, vol.404
, pp. 939-965
-
-
Bantscheff, M.1
Lemeer, S.2
Savitski, M.M.3
Kuster, B.4
-
34
-
-
79551500036
-
Less label, more free: approaches in label-free quantitative mass spectrometry
-
Neilson, K. A., Ali, N. A., Muralidharan, S., Mirzaei, M. et al., Less label, more free: approaches in label-free quantitative mass spectrometry. Proteomics 2011, 11, 535-553.
-
(2011)
Proteomics
, vol.11
, pp. 535-553
-
-
Neilson, K.A.1
Ali, N.A.2
Muralidharan, S.3
Mirzaei, M.4
-
35
-
-
84878075017
-
Statistical methods for quantitative mass spectrometry proteomic experiments with labeling
-
Oberg, A. L., Mahoney, D. W., Statistical methods for quantitative mass spectrometry proteomic experiments with labeling. BMC Bioinformatics 2012, 13, S7.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. S7
-
-
Oberg, A.L.1
Mahoney, D.W.2
-
36
-
-
84882589554
-
Topologically inferring risk-active pathways toward precise cancer classification by directed random walk
-
Liu, W., Li, C., Xu, Y., Yang, H. et al., Topologically inferring risk-active pathways toward precise cancer classification by directed random walk. Bioinformatics 2013, 29, 2169-2177.
-
(2013)
Bioinformatics
, vol.29
, pp. 2169-2177
-
-
Liu, W.1
Li, C.2
Xu, Y.3
Yang, H.4
-
37
-
-
84873987395
-
A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments
-
Matzke, M. M., Brown, J. N., Gritsenko, M. A., Metz, T. O. et al., A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments. Proteomics 2013, 13, 493-503.
-
(2013)
Proteomics
, vol.13
, pp. 493-503
-
-
Matzke, M.M.1
Brown, J.N.2
Gritsenko, M.A.3
Metz, T.O.4
-
38
-
-
40549113310
-
Finding the significant markers: statistical analysis of proteomic data
-
Carpentier, S. C., Panis, B., Swennen, R., Lammertyn, J., Finding the significant markers: statistical analysis of proteomic data. Methods Mol. Biol. Clifton Nj 2008, 428, 327-347.
-
(2008)
Methods Mol. Biol. Clifton Nj
, vol.428
, pp. 327-347
-
-
Carpentier, S.C.1
Panis, B.2
Swennen, R.3
Lammertyn, J.4
-
39
-
-
79952197936
-
Statistics in experimental design, preprocessing, and analysis of proteomics data
-
Jung, K., Statistics in experimental design, preprocessing, and analysis of proteomics data. Methods Mol. Biol. 2011, 696, 259-272.
-
(2011)
Methods Mol. Biol.
, vol.696
, pp. 259-272
-
-
Jung, K.1
-
40
-
-
84925392773
-
A primer to frequent itemset mining for bioinformatics
-
Naulaerts, S., Meysman, P., Bittremieux, W., Vu, T. N. et al., A primer to frequent itemset mining for bioinformatics. Brief. Bioinform. 2013. doi: 10.1093/bib/bbt074.
-
(2013)
Brief. Bioinform.
-
-
Naulaerts, S.1
Meysman, P.2
Bittremieux, W.3
Vu, T.N.4
-
41
-
-
84860833500
-
The UniProt consortium, reorganizing the protein space at the universal protein resource (UniProt)
-
The UniProt consortium, reorganizing the protein space at the universal protein resource (UniProt). Nucleic Acids Res. 2011, 40, D71-D75.
-
(2011)
Nucleic Acids Res.
, vol.40
, pp. D71-D75
-
-
-
42
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D. et al., Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000, 25, 25-29.
-
(2000)
Nat. Genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
-
43
-
-
80053188682
-
Literature-aided interpretation of gene expression data with the weighted global test
-
Jelier, R., Goeman, J. J., Hettne, K. M., Schuemie, M. J. et al., Literature-aided interpretation of gene expression data with the weighted global test. Brief. Bioinform. 2011, 12, 518-529.
-
(2011)
Brief. Bioinform.
, vol.12
, pp. 518-529
-
-
Jelier, R.1
Goeman, J.J.2
Hettne, K.M.3
Schuemie, M.J.4
-
44
-
-
84878483493
-
Biases in the experimental annotations of protein function and their effect on our understanding of protein function space
-
Schnoes, A. M., Ream, D. C., Thorman, A. W., Babbitt, P. C., Friedberg, I., Biases in the experimental annotations of protein function and their effect on our understanding of protein function space. Plos Comput. Biol. 2013, 9, e1003063.
-
(2013)
Plos Comput. Biol.
, vol.9
, pp. e1003063
-
-
Schnoes, A.M.1
Ream, D.C.2
Thorman, A.W.3
Babbitt, P.C.4
Friedberg, I.5
-
45
-
-
84904723024
-
Gene set analysis methods: statistical models and methodological differences
-
Maciejewski, H., Gene set analysis methods: statistical models and methodological differences. Brief. Bioinform. 2014, 15, 504-518.
-
(2014)
Brief. Bioinform.
, vol.15
, pp. 504-518
-
-
Maciejewski, H.1
-
46
-
-
0347513219
-
Characterizing gene sets with FuncAssociate
-
Berriz, G. F., King, O. D., Bryant, B., Sander, C., Roth, F. P., Characterizing gene sets with FuncAssociate. Bioinformatics 2003, 19, 2502-2504.
-
(2003)
Bioinformatics
, vol.19
, pp. 2502-2504
-
-
Berriz, G.F.1
King, O.D.2
Bryant, B.3
Sander, C.4
Roth, F.P.5
-
47
-
-
0035704901
-
Profiling gene expression using onto-express
-
Khatri, P., Draghici, S., Ostermeier, G. C., Krawetz, S. A., Profiling gene expression using onto-express. Genomics 2002, 79, 266-270.
-
(2002)
Genomics
, vol.79
, pp. 266-270
-
-
Khatri, P.1
Draghici, S.2
Ostermeier, G.C.3
Krawetz, S.A.4
-
48
-
-
0038175144
-
GoMiner: a resource for biological interpretation of genomic and proteomic data
-
R28
-
Zeeberg, B. R., Feng, W., Wang, G., Wang, M. D. et al., GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol. 2003, 4, R28.
-
(2003)
Genome Biol.
, vol.4
-
-
Zeeberg, B.R.1
Feng, W.2
Wang, G.3
Wang, M.D.4
-
49
-
-
24044440971
-
BiNGO: 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 2005, 21, 3448-3449.
-
(2005)
Bioinformatics
, vol.21
, pp. 3448-3449
-
-
Maere, S.1
Heymans, K.2
Kuiper, M.3
-
50
-
-
33747846582
-
WEGO: a web tool for plotting GO annotations
-
Ye, J., Fang, L., Zheng, H., Zhang, Y. et al., WEGO: a web tool for plotting GO annotations. Nucleic Acids Res. 2006, 34, W293-297.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. W293-W297
-
-
Ye, J.1
Fang, L.2
Zheng, H.3
Zhang, Y.4
-
51
-
-
34447640967
-
GenMAPP 2: new features and resources for pathway analysis
-
Salomonis, N., Hanspers, K., Zambon, A. C., Vranizan, K. et al., GenMAPP 2: new features and resources for pathway analysis. BMC Bioinformatics 2007, 8, 217.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 217
-
-
Salomonis, N.1
Hanspers, K.2
Zambon, A.C.3
Vranizan, K.4
-
52
-
-
61449172037
-
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
-
Huang, D. W., Sherman, B. T., Lempicki, R. A., Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2008, 4, 44-57.
-
(2008)
Nat. Protoc.
, vol.4
, pp. 44-57
-
-
Huang, D.W.1
Sherman, B.T.2
Lempicki, R.A.3
-
53
-
-
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. 2008, 36, W358-W363.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. W358-W363
-
-
Zheng, Q.1
Wang, X.J.2
-
54
-
-
64549104807
-
ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks
-
Bindea, G., Mlecnik, B., Hackl, H., Charoentong, P. et al., ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 2009, 25, 1091-1093.
-
(2009)
Bioinformatics
, vol.25
, pp. 1091-1093
-
-
Bindea, G.1
Mlecnik, B.2
Hackl, H.3
Charoentong, P.4
-
55
-
-
77954299992
-
agriGO: a GO analysis toolkit for the agricultural community
-
Du, Z., Zhou, X., Ling, Y., Zhang, Z., Su, Z., agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 2010, 38, W64-W70.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. W64-W70
-
-
Du, Z.1
Zhou, X.2
Ling, Y.3
Zhang, Z.4
Su, Z.5
-
56
-
-
77951968341
-
GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach
-
Zhang, S., Cao, J., Kong, Y. M., Scheuermann, R. H., GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach. Bioinformatics 2010, 26, 905-911.
-
(2010)
Bioinformatics
, vol.26
, pp. 905-911
-
-
Zhang, S.1
Cao, J.2
Kong, Y.M.3
Scheuermann, R.H.4
-
57
-
-
84880617636
-
WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013
-
Wang, J., Duncan, D., Shi, Z., Zhang, B., WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. Nucleic Acids Res. 2013, 41, W77-W83.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. W77-W83
-
-
Wang, J.1
Duncan, D.2
Shi, Z.3
Zhang, B.4
-
58
-
-
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 2012, 28, i451-i457.
-
(2012)
Bioinformatics
, vol.28
, pp. i451-i457
-
-
Glaab, E.1
Baudot, A.2
Krasnogor, N.3
Schneider, R.4
Valencia, A.5
-
59
-
-
0035999977
-
A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments
-
Pan, W., A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments. Bioinformatics 2002, 18, 546-554.
-
(2002)
Bioinformatics
, vol.18
, pp. 546-554
-
-
Pan, W.1
-
60
-
-
84871206169
-
Fold change and p-value cutoffs significantly alter microarray interpretations
-
Dalman, M. R., Deeter, A., Nimishakavi, G., Duan, Z. H., Fold change and p-value cutoffs significantly alter microarray interpretations. BMC Bioinformatics 2012, 13, S11.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. S11
-
-
Dalman, M.R.1
Deeter, A.2
Nimishakavi, G.3
Duan, Z.H.4
-
61
-
-
43149116763
-
Gene-set approach for expression pattern analysis
-
Nam, D., Kim, S. Y., Gene-set approach for expression pattern analysis. Brief. Bioinform. 2008, 9, 189-197.
-
(2008)
Brief. Bioinform.
, vol.9
, pp. 189-197
-
-
Nam, D.1
Kim, S.Y.2
-
62
-
-
36448946146
-
Improved detection of overrepresentation of Gene-Ontology annotations with parent-child analysis
-
Grossmann, S., Bauer, S., Robinson, P. N., Vingron, M., Improved detection of overrepresentation of Gene-Ontology annotations with parent-child analysis. Bioinformatics 2007, 23, 3024-3031.
-
(2007)
Bioinformatics
, vol.23
, pp. 3024-3031
-
-
Grossmann, S.1
Bauer, S.2
Robinson, P.N.3
Vingron, M.4
-
63
-
-
40249110012
-
ProLoc-GO: Utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization
-
Huang, W. L., Tung, C. W., Ho, S. W., Hwang, S. F., Ho, S. Y., ProLoc-GO: Utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization. BMC Bioinformatics 2008, 9, 80.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 80
-
-
Huang, W.L.1
Tung, C.W.2
Ho, S.W.3
Hwang, S.F.4
Ho, S.Y.5
-
64
-
-
77953212372
-
Gene ontology analysis for RNA-seq: accounting for selection bias
-
R14
-
Young, M. D., Wakefield, M. J., Smyth, G. K., Oshlack, A., Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol. 2010, 11, R14.
-
(2010)
Genome Biol.
, vol.11
-
-
Young, M.D.1
Wakefield, M.J.2
Smyth, G.K.3
Oshlack, A.4
-
65
-
-
26844457138
-
Pancreatic cancer proteome: the proteins that underlie invasion, metastasis, and immunologic escape
-
Chen, R., Yi, E. C., Donohoe, S., Pan, S. et al., Pancreatic cancer proteome: the proteins that underlie invasion, metastasis, and immunologic escape. Gastroenterology 2005, 129, 1187-1197.
-
(2005)
Gastroenterology
, vol.129
, pp. 1187-1197
-
-
Chen, R.1
Yi, E.C.2
Donohoe, S.3
Pan, S.4
-
66
-
-
84901599553
-
A draft map of the human proteome
-
Kim, M. S., Pinto, S. M., Getnet, D., Nirujogi, R. 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
-
67
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S. et al., Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 15545-15550.
-
(2005)
Proc. Natl. Acad. Sci. U. S. A.
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, S.4
-
68
-
-
35548988505
-
Computation of significance scores of unweighted Gene Set Enrichment Analyses
-
Keller, A., Backes, C., Lenhof, H. P., Computation of significance scores of unweighted Gene Set Enrichment Analyses. BMC Bioinformatics 2007, 8, 290.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 290
-
-
Keller, A.1
Backes, C.2
Lenhof, H.P.3
-
69
-
-
84893380809
-
Human cognitive ability is influenced by genetic variation in components of postsynaptic signalling complexes assembled by NMDA receptors and MAGUK proteins
-
Hill, W. D., Davies, G., van de Lagemaat, L. N., Christoforou, A. et al., Human cognitive ability is influenced by genetic variation in components of postsynaptic signalling complexes assembled by NMDA receptors and MAGUK proteins. Transl. Psychiatry 2014, 4, e341.
-
(2014)
Transl. Psychiatry
, vol.4
, pp. e341
-
-
Hill, W.D.1
Davies, G.2
van de Lagemaat, L.N.3
Christoforou, A.4
-
70
-
-
78149289532
-
In Situ proteomic analysis of human breast cancer epithelial cells using laser capture microdissection (LCM)-LC/MS: Annotation by protein set enrichment analysis (PSEA) and gene ontology (GO)
-
mcp.M110.000398.
-
Cha, S., Imielinski, M. B., Rejtar, T., Richardson, E. A. et al., In Situ proteomic analysis of human breast cancer epithelial cells using laser capture microdissection (LCM)-LC/MS: Annotation by protein set enrichment analysis (PSEA) and gene ontology (GO). Mol. Cell. Proteomics 2010, mcp.M110.000398.
-
(2010)
Mol. Cell. Proteomics
-
-
Cha, S.1
Imielinski, M.B.2
Rejtar, T.3
Richardson, E.A.4
-
71
-
-
58149203231
-
InterPro: the integrative protein signature database
-
Hunter, S., Apweiler, R., Attwood, T. K., Bairoch, A. et al., InterPro: the integrative protein signature database. Nucleic Acids Res. 2009, 37, D211-D215.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D211-D215
-
-
Hunter, S.1
Apweiler, R.2
Attwood, T.K.3
Bairoch, A.4
-
72
-
-
84891760956
-
Data, information, knowledge and principle: back to metabolism in KEGG
-
Kanehisa, M., Goto, S., Sato, Y., Kawashima, M. et al., Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 2014, 42, D199-D205.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D199-D205
-
-
Kanehisa, M.1
Goto, S.2
Sato, Y.3
Kawashima, M.4
-
73
-
-
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 2005, 6, 225.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 225
-
-
Tomfohr, J.1
Lu, J.2
Kepler, T.B.3
-
74
-
-
33748198771
-
Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles
-
Edelman, E., Porrello, A., Guinney, J., Balakumaran, B. et al., Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles. Bioinformatics 2006, 22, e108-e116.
-
(2006)
Bioinformatics
, vol.22
, pp. e108-e116
-
-
Edelman, E.1
Porrello, A.2
Guinney, J.3
Balakumaran, B.4
-
75
-
-
34547840192
-
GAzer: gene set analyzer
-
Kim, S. B., Yang, S., Kim, S. K., Kim, S. C. et al., GAzer: gene set analyzer. Bioinformatics 2007, 23, 1697-1699.
-
(2007)
Bioinformatics
, vol.23
, pp. 1697-1699
-
-
Kim, S.B.1
Yang, S.2
Kim, S.K.3
Kim, S.C.4
-
76
-
-
26444608611
-
Discovering statistically significant pathways in expression profiling studies
-
Tian, L., Greenberg, S. A., Kong, S. W., Altschuler, J. et al., Discovering statistically significant pathways in expression profiling studies. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 13544-13549.
-
(2005)
Proc. Natl. Acad. Sci. U. S. A.
, vol.102
, pp. 13544-13549
-
-
Tian, L.1
Greenberg, S.A.2
Kong, S.W.3
Altschuler, J.4
-
77
-
-
0001677717
-
Controlling the false discovery rate: a practical and powerful approach to multiple testing
-
Benjamini, Y., Hochberg, Y., Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Methodol. 1995, 57, 289-300.
-
(1995)
J. R. Stat. Soc. Ser. B Methodol.
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
78
-
-
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 2013, 8, e79217.
-
(2013)
Plos One
, vol.8
, pp. e79217
-
-
Tarca, A.L.1
Bhatti, G.2
Romero, R.3
-
79
-
-
13444274300
-
MEGO: gene functional module expression based on gene ontology
-
Tu, K., Yu, H., Zhu, M., MEGO: gene functional module expression based on gene ontology. Biotechniques 2005, 38, 277-283.
-
(2005)
Biotechniques
, vol.38
, pp. 277-283
-
-
Tu, K.1
Yu, H.2
Zhu, M.3
-
80
-
-
25444502609
-
PAGE: parametric analysis of gene set enrichment
-
Kim, S. Y., Volsky, D. J., PAGE: parametric analysis of gene set enrichment. BMC Bioinformatics 2005, 6, 144.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 144
-
-
Kim, S.Y.1
Volsky, D.J.2
-
81
-
-
34247354150
-
From genes to functional classes in the study of biological systems
-
Al-Shahrour, F., Arbiza, L., Dopazo, H., Huerta-Cepas, J. et al., From genes to functional classes in the study of biological systems. BMC Bioinformatics 2007, 8, 114.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 114
-
-
Al-Shahrour, F.1
Arbiza, L.2
Dopazo, H.3
Huerta-Cepas, J.4
-
82
-
-
67649202800
-
GAGE: generally applicable gene set enrichment for pathway analysis
-
161.
-
Luo, W., Friedman, M. S., Shedden, K., Hankenson, K. D., Woolf, P. J., GAGE: generally applicable gene set enrichment for pathway analysis. BMC Bioinformatics 2009, 10, 161.
-
(2009)
BMC Bioinformatics
, vol.10
-
-
Luo, W.1
Friedman, M.S.2
Shedden, K.3
Hankenson, K.D.4
Woolf, P.J.5
-
83
-
-
0038054341
-
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
-
Mootha, V. K., Lindgren, C. M., Eriksson, K. F., Subramanian, A. et al., PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet. 2003, 34, 267-273.
-
(2003)
Nat. Genet.
, vol.34
, pp. 267-273
-
-
Mootha, V.K.1
Lindgren, C.M.2
Eriksson, K.F.3
Subramanian, A.4
-
84
-
-
84861793773
-
Gene set enrichment analysis: performance evaluation and usage guidelines
-
Hung, J. H., Yang, T. H., Hu, Z., Weng, Z., DeLisi, C., Gene set enrichment analysis: performance evaluation and usage guidelines. Brief. Bioinform. 2012, 13, 281-291.
-
(2012)
Brief. Bioinform.
, vol.13
, pp. 281-291
-
-
Hung, J.H.1
Yang, T.H.2
Hu, Z.3
Weng, Z.4
DeLisi, C.5
-
85
-
-
60749090295
-
Gene-set analysis and reduction
-
Dinu, I., Potter, J. D., Mueller, T., Liu, Q. et al., Gene-set analysis and reduction. Brief. Bioinform. 2009, 10, 24-34.
-
(2009)
Brief. Bioinform.
, vol.10
, pp. 24-34
-
-
Dinu, I.1
Potter, J.D.2
Mueller, T.3
Liu, Q.4
-
86
-
-
77956524952
-
De-correlating expression in gene-set analysis
-
Nam, D., De-correlating expression in gene-set analysis. Bioinformatics 2010, 26, i511-i516.
-
(2010)
Bioinformatics
, vol.26
, pp. i511-i516
-
-
Nam, D.1
-
87
-
-
84861123691
-
Ten years of pathway analysis: current approaches and outstanding challenges
-
Khatri, P., Sirota, M., Butte, A. J., Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput. Biol. 2012, 8, e1002375.
-
(2012)
PLoS Comput. Biol.
, vol.8
, pp. e1002375
-
-
Khatri, P.1
Sirota, M.2
Butte, A.J.3
-
88
-
-
84880544162
-
Gene-set analysis is severely biased when applied to genome-wide methylation data
-
Geeleher, P., Hartnett, L., Egan, L. J., Golden, A. et al., Gene-set analysis is severely biased when applied to genome-wide methylation data. Bioinformatics 2013, 29, 1851-1857.
-
(2013)
Bioinformatics
, vol.29
, pp. 1851-1857
-
-
Geeleher, P.1
Hartnett, L.2
Egan, L.J.3
Golden, A.4
-
89
-
-
47349105353
-
Anni 2.0: a multipurpose text-mining tool for the life sciences
-
R96
-
Jelier, R., Schuemie, M. J., Veldhoven, A., Dorssers, L. C. et al., Anni 2.0: a multipurpose text-mining tool for the life sciences. Genome Biol. 2008, 9, R96.
-
(2008)
Genome Biol.
, vol.9
-
-
Jelier, R.1
Schuemie, M.J.2
Veldhoven, A.3
Dorssers, L.C.4
-
90
-
-
70849127582
-
Novel protein-protein interactions inferred from literature context
-
Van Haagen, H. H. H. B. M., 't Hoen, P. A. C., Botelho Bovo, A., de Morrée, A. et al., Novel protein-protein interactions inferred from literature context. PLoS One 2009, 4, e7894.
-
(2009)
PLoS One
, vol.4
, pp. e7894
-
-
Van Haagen, H.H.H.B.M.1
't Hoen, P.A.C.2
Botelho Bovo, A.3
de Morrée, A.4
-
91
-
-
0038017587
-
Mining microarray expression data by literature profiling
-
research0055.1-research0055.16.
-
Chaussabel, D., Sher, A., Mining microarray expression data by literature profiling. Genome Biol. 2002, 3, research0055.1-research0055.16.
-
(2002)
Genome Biol.
, vol.3
-
-
Chaussabel, D.1
Sher, A.2
-
92
-
-
25444530343
-
CoPub Mapper: mining MEDLINE based on search term co-publication
-
Alako, B. T., Veldhoven, A., Baal, S. van, Jelier, R. et al., CoPub Mapper: mining MEDLINE based on search term co-publication. BMC Bioinformatics 2005, 6, 51.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 51
-
-
Alako, B.T.1
Veldhoven, A.2
Baal, S.v.3
Jelier, R.4
-
93
-
-
75649097434
-
Martini: using literature keywords to compare gene sets
-
Soldatos, T. G., O'Donoghue, S. I., Satagopam, V. P., Jensen, L. J. et al., Martini: using literature keywords to compare gene sets. Nucleic Acids Res. 2010, 38, 26-38.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 26-38
-
-
Soldatos, T.G.1
O'Donoghue, S.I.2
Satagopam, V.P.3
Jensen, L.J.4
-
94
-
-
84907030251
-
GenCLiP 2.0: a web server for functional clustering of genes and construction of molecular networks based on free terms
-
Wang, J. H., Zhao, L. F., Lin, P., Su, X. R. et al., GenCLiP 2.0: a web server for functional clustering of genes and construction of molecular networks based on free terms. Bioinformatics 2014, 30, 2534-2536.
-
(2014)
Bioinformatics
, vol.30
, pp. 2534-2536
-
-
Wang, J.H.1
Zhao, L.F.2
Lin, P.3
Su, X.R.4
-
95
-
-
0035042776
-
A literature network of human genes for high-throughput analysis of gene expression
-
Jenssen, T. K., Laegreid, A., Komorowski, J., Hovig, E., A literature network of human genes for high-throughput analysis of gene expression. Nat. Genet. 2001, 28, 21-28.
-
(2001)
Nat. Genet.
, vol.28
, pp. 21-28
-
-
Jenssen, T.K.1
Laegreid, A.2
Komorowski, J.3
Hovig, E.4
-
96
-
-
4844222294
-
TXTGate: profiling gene groups with text-based information
-
R43
-
Glenisson, P., Coessens, B., Vooren, S. V., Mathys, J. et al., TXTGate: profiling gene groups with text-based information. Genome Biol. 2004, 5, R43.
-
(2004)
Genome Biol.
, vol.5
-
-
Glenisson, P.1
Coessens, B.2
Vooren, S.V.3
Mathys, J.4
-
97
-
-
77957703420
-
Discovering gene functional relationships using FAUN (Feature Annotation Using Nonnegative matrix factorization)
-
Tjioe, E., Berry, M. W., Homayouni, R., Discovering gene functional relationships using FAUN (Feature Annotation Using Nonnegative matrix factorization). BMC Bioinformatics 2010, 11, S14.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. S14
-
-
Tjioe, E.1
Berry, M.W.2
Homayouni, R.3
-
98
-
-
77949510039
-
LAITOR-literature assistant for identification of terms co-occurrences and relationships
-
Barbosa-Silva, A., Soldatos, T. G., Magalhães, I. L., Pavlopoulos, G. A. et al., LAITOR-literature assistant for identification of terms co-occurrences and relationships. BMC Bioinformatics 2010, 11, 70.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 70
-
-
Barbosa-Silva, A.1
Soldatos, T.G.2
Magalhães, I.L.3
Pavlopoulos, G.A.4
-
99
-
-
82455162310
-
PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries
-
Barbosa-Silva, A., Fontaine, J. F., Donnard, E. R., Stussi, F. et al., PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries. BMC Bioinformatics 2011, 12, 435.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 435
-
-
Barbosa-Silva, A.1
Fontaine, J.F.2
Donnard, E.R.3
Stussi, F.4
-
100
-
-
84884507478
-
CoCiter: An efficient tool to infer gene function by assessing the significance of literature co-citation
-
Qiao, N., Huang, Y., Naveed, H., Green, C. D., Han, J. D. J., CoCiter: An efficient tool to infer gene function by assessing the significance of literature co-citation. PLoS One 2013, 8, e74074.
-
(2013)
PLoS One
, vol.8
, pp. e74074
-
-
Qiao, N.1
Huang, Y.2
Naveed, H.3
Green, C.D.4
Han, J.D.J.5
-
101
-
-
79955797347
-
Network-based pipeline for analyzing ms data: an application toward liver cancer
-
Goh, W. W. B., Lee, Y. H., Zubaidah, R. M., Jin, J. et al., Network-based pipeline for analyzing ms data: an application toward liver cancer. J. Proteome Res. 2011, 10, 2261-2272.
-
(2011)
J. Proteome Res.
, vol.10
, pp. 2261-2272
-
-
Goh, W.W.B.1
Lee, Y.H.2
Zubaidah, R.M.3
Jin, J.4
-
102
-
-
84859242507
-
How advancement in biological network analysis methods empowers proteomics
-
Goh, W. W. B., Lee, Y. H., Chung, M., Wong, L., How advancement in biological network analysis methods empowers proteomics. Proteomics 2012, 12, 550-563.
-
(2012)
Proteomics
, vol.12
, pp. 550-563
-
-
Goh, W.W.B.1
Lee, Y.H.2
Chung, M.3
Wong, L.4
-
103
-
-
84872184001
-
Enhancing the utility of proteomics signature profiling (PSP) with pathway derived Subnets (PDSs), performance analysis and specialised ontologies
-
Goh, W. W. B., Fan, M., Low, H. S., Sergot, M., Wong, L., Enhancing the utility of proteomics signature profiling (PSP) with pathway derived Subnets (PDSs), performance analysis and specialised ontologies. BMC Genomics 2013, 14, 35.
-
(2013)
BMC Genomics
, vol.14
, pp. 35
-
-
Goh, W.W.B.1
Fan, M.2
Low, H.S.3
Sergot, M.4
Wong, L.5
-
104
-
-
84887625418
-
Networks in proteomics analysis of cancer
-
Goh, W. W. B., Wong, L., Networks in proteomics analysis of cancer. Curr. Opin. Biotechnol. 2013, 24, 1122-1128.
-
(2013)
Curr. Opin. Biotechnol.
, vol.24
, pp. 1122-1128
-
-
Goh, W.W.B.1
Wong, L.2
-
105
-
-
0242490780
-
Cytoscape: a software environment for integrated models of biomolecular interaction networks
-
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S. et al., 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
-
106
-
-
65449162644
-
A survey of visualization tools for biological network analysis
-
Pavlopoulos, G. A., Wegener, A. L., Schneider, R., A survey of visualization tools for biological network analysis. Biodata Min. 2008, 1, 12.
-
(2008)
Biodata Min.
, vol.1
, pp. 12
-
-
Pavlopoulos, G.A.1
Wegener, A.L.2
Schneider, R.3
-
107
-
-
77649252269
-
Visualization of omics data for systems biology
-
Gehlenborg, N., O'Donoghue, S. I., Baliga, N. S., Goesmann, A. et al., Visualization of omics data for systems biology. Nat. Methods 2010, 7, S56-S68.
-
(2010)
Nat. Methods
, vol.7
, pp. S56-S68
-
-
Gehlenborg, N.1
O'Donoghue, S.I.2
Baliga, N.S.3
Goesmann, A.4
-
108
-
-
69249122100
-
Network-assisted protein identification and data interpretation in shotgun proteomics
-
Li, J., Zimmerman, L. J., Park, B. H., Tabb, D. L. et al., Network-assisted protein identification and data interpretation in shotgun proteomics. Mol. Syst. Biol. 2009, 5.
-
(2009)
Mol. Syst. Biol.
, vol.5
-
-
Li, J.1
Zimmerman, L.J.2
Park, B.H.3
Tabb, D.L.4
-
109
-
-
77952909304
-
Candidate Serological biomarkers for cancer identified from the secretomes of 23 cancer cell lines and the human protein atlas
-
Wu, C. C., Hsu, C. W., Chen, C. D., Yu, C. J. et al., Candidate Serological biomarkers for cancer identified from the secretomes of 23 cancer cell lines and the human protein atlas. Mol. Cell. Proteomics 2010, 9, 1100-1117.
-
(2010)
Mol. Cell. Proteomics
, vol.9
, pp. 1100-1117
-
-
Wu, C.C.1
Hsu, C.W.2
Chen, C.D.3
Yu, C.J.4
-
110
-
-
84862333922
-
Integrated proteomic, transcriptomic, and biological network analysis of breast carcinoma reveals molecular features of tumorigenesis and clinical relapse
-
M111.014910.
-
Imielinski, M., Cha, S., Rejtar, T., Richardson, E. A. et al., Integrated proteomic, transcriptomic, and biological network analysis of breast carcinoma reveals molecular features of tumorigenesis and clinical relapse. Mol. Cell. Proteomics 2012, 11, M111.014910.
-
(2012)
Mol. Cell. Proteomics
, vol.11
-
-
Imielinski, M.1
Cha, S.2
Rejtar, T.3
Richardson, E.A.4
-
111
-
-
79959331909
-
Proteomic patterns of cervical cancer cell lines, a network perspective
-
Higareda-Almaraz, J. C., Enríquez-Gasca, M. R., Hernández-Ortiz, M., Resendis-Antonio, O., Encarnación-Guevara, S., Proteomic patterns of cervical cancer cell lines, a network perspective. BMC Syst. Biol. 2011, 5, 96.
-
(2011)
BMC Syst. Biol.
, vol.5
, pp. 96
-
-
Higareda-Almaraz, J.C.1
Enríquez-Gasca, M.R.2
Hernández-Ortiz, M.3
Resendis-Antonio, O.4
Encarnación-Guevara, S.5
-
112
-
-
77449089538
-
A manually curated network of the PML nuclear body interactome reveals an important role for PML-NBs in SUMOylation dynamics
-
Van Damme, E., Laukens, K., Dang, T. H., Van Ostade, X., A manually curated network of the PML nuclear body interactome reveals an important role for PML-NBs in SUMOylation dynamics. Int. J. Biol. Sci. 2010, 6, 51-67.
-
(2010)
Int. J. Biol. Sci.
, vol.6
, pp. 51-67
-
-
Van Damme, E.1
Laukens, K.2
Dang, T.H.3
Van Ostade, X.4
-
113
-
-
34548400259
-
A systems biology approach for pathway level analysis
-
Draghici, S., Khatri, P., Tarca, A. L., Amin, K. et al., A systems biology approach for pathway level analysis. Genome Res. 2007, 17, 1537-1545.
-
(2007)
Genome Res.
, vol.17
, pp. 1537-1545
-
-
Draghici, S.1
Khatri, P.2
Tarca, A.L.3
Amin, K.4
-
114
-
-
77956480115
-
Consistency, comprehensiveness, and compatibility of pathway databases
-
Soh, D., Dong, D., Guo, Y., Wong, L., Consistency, comprehensiveness, and compatibility of pathway databases. BMC Bioinformatics 2010, 11, 449.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 449
-
-
Soh, D.1
Dong, D.2
Guo, Y.3
Wong, L.4
-
115
-
-
35748935228
-
Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases
-
Cavalieri, D., Castagnini, C., Toti, S., Maciag, K. et al., Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases. Bioinforma. Oxf. Engl. 2007, 23, 2631-2632.
-
(2007)
Bioinforma. Oxf. Engl.
, vol.23
, pp. 2631-2632
-
-
Cavalieri, D.1
Castagnini, C.2
Toti, S.3
Maciag, K.4
-
116
-
-
84891540477
-
Pathway-GPS and SIGORA: identifying relevant pathways based on the over-representation of their gene-pair signatures
-
Foroushani, A. B. K., Brinkman, F. S. L., Lynn, D. J., Pathway-GPS and SIGORA: identifying relevant pathways based on the over-representation of their gene-pair signatures. PeerJ 2013, 1, e229.
-
(2013)
PeerJ
, vol.1
, pp. e229
-
-
Foroushani, A.B.K.1
Brinkman, F.S.L.2
Lynn, D.J.3
-
117
-
-
84876090381
-
Pathway Distiller-multisource biological pathway consolidation
-
Doderer, M. S., Anguiano, Z., Suresh, U., Dashnamoorthy, R. et al., Pathway Distiller-multisource biological pathway consolidation. BMC Genomics 2012, 13, 1-16.
-
(2012)
BMC Genomics
, vol.13
, pp. 1-16
-
-
Doderer, M.S.1
Anguiano, Z.2
Suresh, U.3
Dashnamoorthy, R.4
-
118
-
-
58149177166
-
Reactome knowledgebase of human biological pathways and processes
-
Matthews, L., Gopinath, G., Gillespie, M., Caudy, M. et al., Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 2009, 37, D619-622.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D619-D622
-
-
Matthews, L.1
Gopinath, G.2
Gillespie, M.3
Caudy, M.4
-
119
-
-
48349105261
-
WikiPathways: pathway editing for the People
-
Pico, A. R., Kelder, T., van Iersel, M. P., Hanspers, K. et al., WikiPathways: pathway editing for the People. PLoS Biol 2008, 6, e184.
-
(2008)
PLoS Biol
, vol.6
, pp. e184
-
-
Pico, A.R.1
Kelder, T.2
van Iersel, M.P.3
Hanspers, K.4
-
120
-
-
27244436714
-
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes
-
Karp, P. D., Ouzounis, C. A., Moore-Kochlacs, C., Goldovsky, L. et al., Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res. 2005, 33, 6083-6089.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 6083-6089
-
-
Karp, P.D.1
Ouzounis, C.A.2
Moore-Kochlacs, C.3
Goldovsky, L.4
-
121
-
-
78651332286
-
Pathway Commons, a web resource for biological pathway data
-
Cerami, E. G., Gross, B. E., Demir, E., Rodchenkov, I. et al., Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. 2011, 39, D685-D690.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D685-D690
-
-
Cerami, E.G.1
Gross, B.E.2
Demir, E.3
Rodchenkov, I.4
-
122
-
-
84874969184
-
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees
-
Mi, H., Muruganujan, A., Thomas, P. D., PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res. 2013, 41, D377-D386.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D377-D386
-
-
Mi, H.1
Muruganujan, A.2
Thomas, P.D.3
-
123
-
-
14644430468
-
Calculating the statistical significance of changes in pathway activity from gene expression data
-
Rahnenführer, J., Domingues, F. S., Maydt, J., Lengauer, T., Calculating the statistical significance of changes in pathway activity from gene expression data. Stat. Appl. Genet. Mol. Biol. 2004, 3, 1-29.
-
(2004)
Stat. Appl. Genet. Mol. Biol.
, vol.3
, pp. 1-29
-
-
Rahnenführer, J.1
Domingues, F.S.2
Maydt, J.3
Lengauer, T.4
-
124
-
-
84866495994
-
PathNet: a tool for pathway analysis using topological information
-
Dutta, B., Wallqvist, A., Reifman, J., PathNet: a tool for pathway analysis using topological information. Source Code Biol. Med. 2012, 7, 10.
-
(2012)
Source Code Biol. Med.
, vol.7
, pp. 10
-
-
Dutta, B.1
Wallqvist, A.2
Reifman, J.3
-
125
-
-
58049215467
-
A novel signaling pathway impact analysis
-
Tarca, A. L., Draghici, S., Khatri, P., Hassan, S. S. et al., A novel signaling pathway impact analysis. Bioinformatics 2009, 25, 75-82.
-
(2009)
Bioinformatics
, vol.25
, pp. 75-82
-
-
Tarca, A.L.1
Draghici, S.2
Khatri, P.3
Hassan, S.S.4
-
126
-
-
77949365759
-
Identification of functional modules that correlate with phenotypic difference: the influence of network topology
-
R23
-
Hung, J. H., Whitfield, T. W., Yang, T. H., Hu, Z. et al., Identification of functional modules that correlate with phenotypic difference: the influence of network topology. Genome Biol. 2010, 11, R23.
-
(2010)
Genome Biol.
, vol.11
-
-
Hung, J.H.1
Whitfield, T.W.2
Yang, T.H.3
Hu, Z.4
-
127
-
-
61749083981
-
Analysis of Gene Sets Based on the Underlying Regulatory Network
-
Shojaie, A., Michailidis, G., Analysis of Gene Sets Based on the Underlying Regulatory Network. J. Comput. Biol. 2009, 16, 407-426.
-
(2009)
J. Comput. Biol.
, vol.16
, pp. 407-426
-
-
Shojaie, A.1
Michailidis, G.2
-
128
-
-
84866238676
-
Gains in Power from Structured Two-Sample Tests of Means on Graphs
-
Jacob, L., Neuvial, P., Dudoit, S., Gains in Power from Structured Two-Sample Tests of Means on Graphs. Ann. Appl. Stat. 2012, 6, 561-600.
-
(2012)
Ann. Appl. Stat.
, vol.6
, pp. 561-600
-
-
Jacob, L.1
Neuvial, P.2
Dudoit, S.3
-
129
-
-
84893009656
-
Methods and approaches in the topology-based analysis of biological pathways
-
Mitrea, C., Taghavi, Z., Bokanizad, B., Hanoudi, S. et al., Methods and approaches in the topology-based analysis of biological pathways. Front. Physiol. 2013, 4, 278.
-
(2013)
Front. Physiol.
, vol.4
, pp. 278
-
-
Mitrea, C.1
Taghavi, Z.2
Bokanizad, B.3
Hanoudi, S.4
-
130
-
-
77955505357
-
Protein-Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks
-
De Las Rivas, J., Fontanillo, C., Protein-Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks. Plos Comput Biol 2010, 6, e1000807.
-
(2010)
Plos Comput Biol
, vol.6
, pp. e1000807
-
-
De Las Rivas, J.1
Fontanillo, C.2
-
131
-
-
84864092600
-
A quick guide to biomolecular network studies: Construction, analysis, applications, and resources
-
Tang, H., Zhong, F., Xie, H., A quick guide to biomolecular network studies: Construction, analysis, applications, and resources. Biochem. Biophys. Res. Commun. 2012, 424, 7-11.
-
(2012)
Biochem. Biophys. Res. Commun.
, vol.424
, pp. 7-11
-
-
Tang, H.1
Zhong, F.2
Xie, H.3
-
132
-
-
0036088133
-
DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions
-
Xenarios, I., Salwínski, L., Duan, X. J., Higney, P. et al., DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 2002, 30, 303-305.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 303-305
-
-
Xenarios, I.1
Salwínski, L.2
Duan, X.J.3
Higney, P.4
-
133
-
-
58149193222
-
Human protein reference database-2009 update
-
Keshava Prasad, T. S., Goel, R., Kandasamy, K., Keerthikumar, S. et al., Human protein reference database-2009 update. Nucleic Acids Res. 2009, 37, D767-D772.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D767-D772
-
-
Keshava Prasad, T.S.1
Goel, R.2
Kandasamy, K.3
Keerthikumar, S.4
-
134
-
-
78651328883
-
The BioGRID Interaction Database: 2011 update
-
Stark, C., Breitkreutz, B. J., Chatr-aryamontri, A., Boucher, L. et al., The BioGRID Interaction Database: 2011 update. Nucleic Acids Res. 2011, 39, D698-D704.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D698-D704
-
-
Stark, C.1
Breitkreutz, B.J.2
Chatr-aryamontri, A.3
Boucher, L.4
-
135
-
-
84859204939
-
The IntAct molecular interaction database in 2012
-
Kerrien, S., Aranda, B., Breuza, L., Bridge, A. et al., The IntAct molecular interaction database in 2012. Nucleic Acids Res. 2012, 40, D841-D846.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D841-D846
-
-
Kerrien, S.1
Aranda, B.2
Breuza, L.3
Bridge, A.4
-
136
-
-
84860918589
-
MINT, the molecular interaction database: 2012 update
-
Licata, L., Briganti, L., Peluso, D., Perfetto, L. et al., MINT, the molecular interaction database: 2012 update. Nucleic Acids Res. 2012, 40, D857-D861.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D857-D861
-
-
Licata, L.1
Briganti, L.2
Peluso, D.3
Perfetto, L.4
-
137
-
-
77949431355
-
Lists2Networks: Integrated analysis of gene/protein lists
-
Lachmann, A., Ma'ayan, A., Lists2Networks: Integrated analysis of gene/protein lists. BMC Bioinformatics 2010, 11, 87.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 87
-
-
Lachmann, A.1
Ma'ayan, A.2
-
138
-
-
84856918212
-
HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores
-
Schaefer, M. H., Fontaine, J. F., Vinayagam, A., Porras, P. et al., HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores. PLoS One 2012, 7, e31826.
-
(2012)
PLoS One
, vol.7
, pp. e31826
-
-
Schaefer, M.H.1
Fontaine, J.F.2
Vinayagam, A.3
Porras, P.4
-
139
-
-
84876100615
-
Enrichr : interactive and collaborative HTML5 gene list enrichment analysis tool
-
Chen, E. Y., Tan, C. M., Kou, Y., Duan, Q. et al., Enrichr : interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics 2013, 14, 128.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 128
-
-
Chen, E.Y.1
Tan, C.M.2
Kou, Y.3
Duan, Q.4
-
140
-
-
65549102777
-
Protein-protein interaction databases: keeping up with growing interactomes
-
Lehne, B., Schlitt, T., Protein-protein interaction databases: keeping up with growing interactomes. Hum. Genomics 2009, 3, 291-297.
-
(2009)
Hum. Genomics
, vol.3
, pp. 291-297
-
-
Lehne, B.1
Schlitt, T.2
-
141
-
-
84891799734
-
The MIntAct project-IntAct as a common curation platform for 11 molecular interaction databases
-
Orchard, S., Ammari, M., Aranda, B., Breuza, L. et al., The MIntAct project-IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res. 2014, 42, D358-D363.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D358-D363
-
-
Orchard, S.1
Ammari, M.2
Aranda, B.3
Breuza, L.4
-
142
-
-
84876515907
-
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
-
Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M. et al., STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 2013, 41, D808-D815.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D808-D815
-
-
Franceschini, A.1
Szklarczyk, D.2
Frankild, S.3
Kuhn, M.4
-
143
-
-
80052844300
-
The representation of protein complexes in the Protein Ontology (PRO)
-
Bult, C. J., Drabkin, H. J., Evsikov, A., Natale, D. et al., The representation of protein complexes in the Protein Ontology (PRO). BMC Bioinformatics 2011, 12, 371.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 371
-
-
Bult, C.J.1
Drabkin, H.J.2
Evsikov, A.3
Natale, D.4
-
144
-
-
84910679144
-
Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database
-
Khoury, G. A., Baliban, R. C., Floudas, C. A., Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database. Sci. Reports 2011, 1.
-
(2011)
Sci. Reports
, vol.1
-
-
Khoury, G.A.1
Baliban, R.C.2
Floudas, C.A.3
-
145
-
-
84902031172
-
Evolution and functional cross-talk of protein post-translational modifications
-
Beltrao, P., Bork, P., Krogan, N. J., van Noort, V., Evolution and functional cross-talk of protein post-translational modifications. Mol. Syst. Biol. 2013, 9, 714.
-
(2013)
Mol. Syst. Biol.
, vol.9
, pp. 714
-
-
Beltrao, P.1
Bork, P.2
Krogan, N.J.3
van Noort, V.4
-
146
-
-
84864184970
-
Deciphering a global network of functionally associated post-translational modifications
-
Minguez, P., Parca, L., Diella, F., Mende, D. R. et al., Deciphering a global network of functionally associated post-translational modifications. Mol. Syst. Biol. 2012, 8, 599.
-
(2012)
Mol. Syst. Biol.
, vol.8
, pp. 599
-
-
Minguez, P.1
Parca, L.2
Diella, F.3
Mende, D.R.4
-
147
-
-
77953292595
-
Post-translational modifications in signal integration
-
Deribe, Y. L., Pawson, T., Dikic, I., Post-translational modifications in signal integration. Nat. Struct. Mol. Biol. 2010, 17, 666-672.
-
(2010)
Nat. Struct. Mol. Biol.
, vol.17
, pp. 666-672
-
-
Deribe, Y.L.1
Pawson, T.2
Dikic, I.3
-
148
-
-
77952956167
-
Decoding signalling networks by mass spectrometry-based proteomics
-
Choudhary, C., Mann, M., Decoding signalling networks by mass spectrometry-based proteomics. Nat. Rev. Mol. Cell Biol. 2010, 11, 427-439.
-
(2010)
Nat. Rev. Mol. Cell Biol.
, vol.11
, pp. 427-439
-
-
Choudhary, C.1
Mann, M.2
-
149
-
-
33644876212
-
dbPTM: an information repository of protein post-translational modification
-
Lee, T. Y., dbPTM: an information repository of protein post-translational modification. Nucleic Acids Res. 2006, 34, D622-D627.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. D622-D627
-
-
Lee, T.Y.1
-
150
-
-
78651277460
-
PHOSIDA 2011: the posttranslational modification database
-
Gnad, F., Gunawardena, J., Mann, M., PHOSIDA 2011: the posttranslational modification database. Nucleic Acids Res. 2010, 39, D253-D260.
-
(2010)
Nucleic Acids Res.
, vol.39
, pp. D253-D260
-
-
Gnad, F.1
Gunawardena, J.2
Mann, M.3
-
151
-
-
78651320816
-
Phospho.ELM: a database of phosphorylation sites-update 2011
-
Dinkel, H., Chica, C., Via, A., Gould, C. M. et al., Phospho.ELM: a database of phosphorylation sites-update 2011. Nucleic Acids Res. 2010, 39, D261-D267.
-
(2010)
Nucleic Acids Res.
, vol.39
, pp. D261-D267
-
-
Dinkel, H.1
Chica, C.2
Via, A.3
Gould, C.M.4
-
152
-
-
84857047339
-
PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse
-
Hornbeck, P. V., Kornhauser, J. M., Tkachev, S., Zhang, B. et al., PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 2012, 40, D261-D270.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D261-D270
-
-
Hornbeck, P.V.1
Kornhauser, J.M.2
Tkachev, S.3
Zhang, B.4
-
153
-
-
84901788851
-
KinomeXplorer: an integrated platform for kinome biology studies
-
Horn, H., Schoof, E. M., Kim, J., Robin, X. et al., KinomeXplorer: an integrated platform for kinome biology studies. Nat. Methods 2014, 11, 603-604.
-
(2014)
Nat. Methods
, vol.11
, pp. 603-604
-
-
Horn, H.1
Schoof, E.M.2
Kim, J.3
Robin, X.4
-
154
-
-
65149105339
-
A post-translational modification code for transcription factors: sorting through a sea of signals
-
Benayoun, B. A., Veitia, R. A., A post-translational modification code for transcription factors: sorting through a sea of signals. Trends Cell Biol. 2009, 19, 189-197.
-
(2009)
Trends Cell Biol.
, vol.19
, pp. 189-197
-
-
Benayoun, B.A.1
Veitia, R.A.2
-
155
-
-
84874957680
-
PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins
-
Minguez, P., Letunic, I., Parca, L., Bork, P., PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins. Nucleic Acids Res. 2013, 41, D306-D311.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D306-D311
-
-
Minguez, P.1
Letunic, I.2
Parca, L.3
Bork, P.4
-
156
-
-
79953044960
-
Genome-wide transcription factor binding: beyond direct target regulation
-
MacQuarrie, K. L., Fong, A. P., Morse, R. H., Tapscott, S. J., Genome-wide transcription factor binding: beyond direct target regulation. Trends Genet. 2011, 27, 141-148.
-
(2011)
Trends Genet.
, vol.27
, pp. 141-148
-
-
MacQuarrie, K.L.1
Fong, A.P.2
Morse, R.H.3
Tapscott, S.J.4
-
157
-
-
34250159524
-
Genome-wide mapping of in vivo protein-dna interactions
-
Johnson, D. S., Mortazavi, A., Myers, R. M., Wold, B., Genome-wide mapping of in vivo protein-dna interactions. Science 2007, 316, 1497-1502.
-
(2007)
Science
, vol.316
, pp. 1497-1502
-
-
Johnson, D.S.1
Mortazavi, A.2
Myers, R.M.3
Wold, B.4
-
158
-
-
46049087782
-
The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation
-
Wingender, E., The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Brief. Bioinform. 2008, 9, 326-332.
-
(2008)
Brief. Bioinform.
, vol.9
, pp. 326-332
-
-
Wingender, E.1
-
159
-
-
7444267933
-
A Gateway-Compatible Yeast One-Hybrid System
-
Deplancke, B., Dupuy, D., Vidal, M., Walhout, A. J. M., A Gateway-Compatible Yeast One-Hybrid System. Genome Res. 2004, 14, 2093-2101.
-
(2004)
Genome Res.
, vol.14
, pp. 2093-2101
-
-
Deplancke, B.1
Dupuy, D.2
Vidal, M.3
Walhout, A.J.M.4
-
160
-
-
33845311536
-
Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping
-
Walhout, A. J. M., Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping. Genome Res. 2006, 16, 1445-1454.
-
(2006)
Genome Res.
, vol.16
, pp. 1445-1454
-
-
Walhout, A.J.M.1
-
161
-
-
62549128139
-
A census of human transcription factors: function, expression and evolution
-
Vaquerizas, J. M., Kummerfeld, S. K., Teichmann, S. A., Luscombe, N. M., A census of human transcription factors: function, expression and evolution. Nat. Rev. Genet. 2009, 10, 252-263.
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 252-263
-
-
Vaquerizas, J.M.1
Kummerfeld, S.K.2
Teichmann, S.A.3
Luscombe, N.M.4
-
162
-
-
63849315606
-
High-resolution DNA-binding specificity analysis of yeast transcription factors
-
Zhu, C., Byers, K. J. R. P., McCord, R. P., Shi, Z. et al., High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res. 2009, 19, 556-566.
-
(2009)
Genome Res.
, vol.19
, pp. 556-566
-
-
Zhu, C.1
Byers, K.J.R.P.2
McCord, R.P.3
Shi, Z.4
-
163
-
-
77950920903
-
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
-
Hafner, M., Landthaler, M., Burger, L., Khorshid, M. et al., Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 2010, 141, 129-141.
-
(2010)
Cell
, vol.141
, pp. 129-141
-
-
Hafner, M.1
Landthaler, M.2
Burger, L.3
Khorshid, M.4
-
164
-
-
77949426688
-
A Novel microRNA and transcription factor mediated regulatory network in schizophrenia
-
Guo, A. Y., Sun, J., Jia, P., Zhao, Z., A Novel microRNA and transcription factor mediated regulatory network in schizophrenia. BMC Syst. Biol. 2010, 4, 10.
-
(2010)
BMC Syst. Biol.
, vol.4
, pp. 10
-
-
Guo, A.Y.1
Sun, J.2
Jia, P.3
Zhao, Z.4
-
165
-
-
77949875682
-
MicroRNA control of signal transduction
-
Inui, M., Martello, G., Piccolo, S., MicroRNA control of signal transduction. Nat. Rev. Mol. Cell Biol. 2010, 11, 252-263.
-
(2010)
Nat. Rev. Mol. Cell Biol.
, vol.11
, pp. 252-263
-
-
Inui, M.1
Martello, G.2
Piccolo, S.3
-
166
-
-
14044251458
-
Human MicroRNA Targets
-
John, B., Enright, A. J., Aravin, A., Tuschl, T. et al., Human MicroRNA Targets. PLoS Biol 2004, 2, e363.
-
(2004)
PLoS Biol
, vol.2
, pp. e363
-
-
John, B.1
Enright, A.J.2
Aravin, A.3
Tuschl, T.4
-
167
-
-
11844278458
-
Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets
-
Lewis, B. P., Burge, C. B., Bartel, D. P., Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets. Cell 2005, 120, 15-20.
-
(2005)
Cell
, vol.120
, pp. 15-20
-
-
Lewis, B.P.1
Burge, C.B.2
Bartel, D.P.3
-
168
-
-
34748821761
-
The role of site accessibility in microRNA target recognition
-
Kertesz, M., Iovino, N., Unnerstall, U., Gaul, U., Segal, E., The role of site accessibility in microRNA target recognition. Nat. Genet. 2007, 39, 1278-1284.
-
(2007)
Nat. Genet.
, vol.39
, pp. 1278-1284
-
-
Kertesz, M.1
Iovino, N.2
Unnerstall, U.3
Gaul, U.4
Segal, E.5
-
169
-
-
33746061228
-
Function of the MAPK scaffold protein, Ste5, requires a cryptic PH domain
-
Garrenton, L. S., Young, S. L., Thorner, J., Function of the MAPK scaffold protein, Ste5, requires a cryptic PH domain. Genes Dev. 2006, 20, 1946-1958.
-
(2006)
Genes Dev.
, vol.20
, pp. 1946-1958
-
-
Garrenton, L.S.1
Young, S.L.2
Thorner, J.3
-
170
-
-
79955770162
-
Scaffold Proteins: Hubs for Controlling the Flow of Cellular Information
-
Good, M. C., Zalatan, J. G., Lim, W. A., Scaffold Proteins: Hubs for Controlling the Flow of Cellular Information. Science 2011, 332, 680-686.
-
(2011)
Science
, vol.332
, pp. 680-686
-
-
Good, M.C.1
Zalatan, J.G.2
Lim, W.A.3
-
171
-
-
84891781052
-
STITCH 4: integration of protein-chemical interactions with user data
-
Kuhn, M., Szklarczyk, D., Pletscher-Frankild, S., Blicher, T. H. et al., STITCH 4: integration of protein-chemical interactions with user data. Nucleic Acids Res. 2014, 42, D401-D407.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D401-D407
-
-
Kuhn, M.1
Szklarczyk, D.2
Pletscher-Frankild, S.3
Blicher, T.H.4
-
172
-
-
79958139420
-
Next generation functional proteomics in non-model plants: A survey on techniques and applications for the analysis of protein complexes and post-translational modifications
-
Remmerie, N., De Vijlder, T., Laukens, K., Dang, T. H. et al., Next generation functional proteomics in non-model plants: A survey on techniques and applications for the analysis of protein complexes and post-translational modifications. Phytochemistry 2011, 72, 1192-1218.
-
(2011)
Phytochemistry
, vol.72
, pp. 1192-1218
-
-
Remmerie, N.1
De Vijlder, T.2
Laukens, K.3
Dang, T.H.4
-
173
-
-
77952833904
-
BioCarta. Biotech Softw
-
Nishimura, D., BioCarta. Biotech Softw. Internet Rep. 2001, 2, 117-120.
-
(2001)
Internet Rep.
, vol.2
, pp. 117-120
-
-
Nishimura, D.1
-
174
-
-
0037245913
-
BIND: the Biomolecular Interaction Network Database
-
Bader, G. D., Betel, D., Hogue, C. W. V., BIND: the Biomolecular Interaction Network Database. Nucl. Acids Res. 2003, 31, 248-250.
-
(2003)
Nucl. Acids Res.
, vol.31
, pp. 248-250
-
-
Bader, G.D.1
Betel, D.2
Hogue, C.W.V.3
-
175
-
-
84864037265
-
INOH: ontology-based highly structured database of signal transduction pathways
-
bar052-bar052
-
Yamamoto, S., Sakai, N., Nakamura, H., Fukagawa, H. et al., INOH: ontology-based highly structured database of signal transduction pathways. Database 2011, 2011, bar052-bar052.
-
(2011)
Database
, vol.2011
-
-
Yamamoto, S.1
Sakai, N.2
Nakamura, H.3
Fukagawa, H.4
-
176
-
-
84891767394
-
RefSeq: an update on mammalian reference sequences
-
Pruitt, K. D., Brown, G. R., Hiatt, S. M., Thibaud-Nissen, F. et al., RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014, 42, D756-D763.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D756-D763
-
-
Pruitt, K.D.1
Brown, G.R.2
Hiatt, S.M.3
Thibaud-Nissen, F.4
-
177
-
-
3142665525
-
GOstat: find statistically overrepresented Gene Ontologies within a group of genes
-
Beißbarth, T., Speed, T. P., GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 2004, 20, 1464-1465.
-
(2004)
Bioinformatics
, vol.20
, pp. 1464-1465
-
-
Beißbarth, T.1
Speed, T.P.2
-
178
-
-
0345832338
-
A global test for groups of genes: testing association with a clinical outcome
-
Goeman, J. J., Geer, S. A. van de, Kort, F. de, Houwelingen, H. C. van, A global test for groups of genes: testing association with a clinical outcome. Bioinformatics 2004, 20, 93-99.
-
(2004)
Bioinformatics
, vol.20
, pp. 93-99
-
-
Goeman, J.J.1
Geer, S.A.v.d.2
Kort, F.d.3
Houwelingen, H.C.v.4
-
179
-
-
84872202078
-
GSVA: gene set variation analysis for microarray and RNA-seq data
-
Hänzelmann, S., Castelo, R., Guinney, J., GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics 2013, 14, 7.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 7
-
-
Hänzelmann, S.1
Castelo, R.2
Guinney, J.3
-
180
-
-
84878062174
-
Knowledge-based analysis of proteomics data
-
Bessarabova, M., Ishkin, A., JeBailey, L., Nikolskaya, T., Nikolsky, Y., Knowledge-based analysis of proteomics data. BMC Bioinformatics 2012, 13, S13.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. S13
-
-
Bessarabova, M.1
Ishkin, A.2
JeBailey, L.3
Nikolskaya, T.4
Nikolsky, Y.5
-
181
-
-
84875940659
-
Think back: knowledge-based interpretation of high throughput data
-
Farfán, F., Ma, J., Sartor, M. A., Michailidis, G., Jagadish, H. V., Think back: knowledge-based interpretation of high throughput data. BMC Bioinformatics 2012, 13, 1-7.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 1-7
-
-
Farfán, F.1
Ma, J.2
Sartor, M.A.3
Michailidis, G.4
Jagadish, H.V.5
|