-
1
-
-
13444259844
-
Reactome: a knowledgebase of biological pathways
-
540026, 15608231, Database issue
-
Joshi-Tope G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E, de Bono B, Jassal B, Gopinath G, Wu G, Matthews L, Lewis S, Birney E, Stein L. Reactome: a knowledgebase of biological pathways. Nucleic Acids Res 2005, 33(Database issue):D428-32. 540026, 15608231.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Joshi-Tope, G.1
Gillespie, M.2
Vastrik, I.3
D'Eustachio, P.4
Schmidt, E.5
de Bono, B.6
Jassal, B.7
Gopinath, G.8
Wu, G.9
Matthews, L.10
Lewis, S.11
Birney, E.12
Stein, L.13
-
2
-
-
33847064282
-
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
-
10.1186/jbiol36, 1561585, 16762047
-
Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hon GC, Myers CL, Parsons A, Friesen H, Oughtred R, Tong A, Stark C, Ho Y, Botstein D, Andrews B, Boone C, Troyanskya OG, Ideker T, Dolinski K, Batada NN, Tyers M. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. Journal of Biology 2006, 5(4):11+. 10.1186/jbiol36, 1561585, 16762047.
-
(2006)
Journal of Biology
, vol.5
, Issue.4
-
-
Reguly, T.1
Breitkreutz, A.2
Boucher, L.3
Breitkreutz, B.J.4
Hon, G.C.5
Myers, C.L.6
Parsons, A.7
Friesen, H.8
Oughtred, R.9
Tong, A.10
Stark, C.11
Ho, Y.12
Botstein, D.13
Andrews, B.14
Boone, C.15
Troyanskya, O.G.16
Ideker, T.17
Dolinski, K.18
Batada, N.N.19
Tyers, M.20
more..
-
3
-
-
33644874819
-
From genomics to chemical genomics: new developments in KEGG
-
1347464, 16381885, Database issue
-
Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006, 34(Database issue):D354-7. 1347464, 16381885.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Kanehisa, M.1
Goto, S.2
Hattori, M.3
Aoki-Kinoshita, K.F.4
Itoh, M.5
Kawashima, S.6
Katayama, T.7
Araki, M.8
Hirakawa, M.9
-
4
-
-
27144530248
-
Towards a proteome-scale map of the human protein-protein interaction network
-
10.1038/nature04209, 16189514
-
Rual J, et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 2005, 437(7062):1173-8. 10.1038/nature04209, 16189514.
-
(2005)
Nature
, vol.437
, Issue.7062
, pp. 1173-1178
-
-
Rual, J.1
-
5
-
-
0034628508
-
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
-
10.1038/35001009, 10688190
-
Uetz P, Giot L, Cagney G, Mansfield TA, et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403(6770):623-627. 10.1038/35001009, 10688190.
-
(2000)
Nature
, vol.403
, Issue.6770
, pp. 623-627
-
-
Uetz, P.1
Giot, L.2
Cagney, G.3
Mansfield, T.A.4
-
6
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
10.1038/nature02800, 3006441, 15343339
-
Harbison C, Gordon D, Lee T, Rinaldi N, et al. Transcriptional regulatory code of a eukaryotic genome. Nature 2004, 431(7004):99-104. 10.1038/nature02800, 3006441, 15343339.
-
(2004)
Nature
, vol.431
, Issue.7004
, pp. 99-104
-
-
Harbison, C.1
Gordon, D.2
Lee, T.3
Rinaldi, N.4
-
7
-
-
38449088751
-
Inferring cellular networks - a review
-
arkowetz F, Spang R. Inferring cellular networks - a review. BMC Bioinformatics 2007, 8(Suppl 6).
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.SUPPL. 6
-
-
arkowetz, F.1
Spang, R.2
-
9
-
-
0000801240
-
Discovering regulatory and signalling circuits in molecular interaction networks
-
10.1093/bioinformatics/18.suppl_1.S233, 12169552
-
Ideker T, Ozier O, Schwikowski B, Siegel AF. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 2002, 18(Suppl 1):S233-40. 10.1093/bioinformatics/18.suppl_1.S233, 12169552.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Ideker, T.1
Ozier, O.2
Schwikowski, B.3
Siegel, A.F.4
-
10
-
-
46249128543
-
Identifying functional modules in protein-protein interaction networks: an integrated exact approach
-
10.1093/bioinformatics/btn161, 2718639, 18586718
-
Dittrich MT, Klau GW, Rosenwald A, Dandekar T, Muller T. Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics 2008, 24(13):i223-231. 10.1093/bioinformatics/btn161, 2718639, 18586718.
-
(2008)
Bioinformatics
, vol.24
, Issue.13
-
-
Dittrich, M.T.1
Klau, G.W.2
Rosenwald, A.3
Dandekar, T.4
Muller, T.5
-
11
-
-
34548742517
-
Identification of functional modules using network topology and high-throughput data
-
10.1186/1752-0509-1-8, 1839897, 17408515
-
Ulitsky I, Shamir R. Identification of functional modules using network topology and high-throughput data. BMC Syst Biol 2007, 1:8. 10.1186/1752-0509-1-8, 1839897, 17408515.
-
(2007)
BMC Syst Biol
, vol.1
, pp. 8
-
-
Ulitsky, I.1
Shamir, R.2
-
12
-
-
33750353888
-
Reverse engineering cellular networks
-
10.1038/nprot.2006.106, 17406294
-
Margolin AA, Wang K, Lim WK, Kustagi M, Nemenman I, Califano A. Reverse engineering cellular networks. Nature Protocols 2006, 1(2):662-671. 10.1038/nprot.2006.106, 17406294.
-
(2006)
Nature Protocols
, vol.1
, Issue.2
, pp. 662-671
-
-
Margolin, A.A.1
Wang, K.2
Lim, W.K.3
Kustagi, M.4
Nemenman, I.5
Califano, A.6
-
13
-
-
70249108504
-
Genome-wide identification of post-translational modulators of transcription factor activity in human B cells
-
10.1038/nbt.1563, 2753889, 19741643
-
Wang K, Saito M, Bisikirska BC, Alvarez MJ, Lim WK, Rajbhandari P, Shen Q, Nemenman I, Basso K, Margolin AA, Klein U, Dalla-Favera R, Califano A. Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nature Biotechnology 2009, 27(9):829-837. 10.1038/nbt.1563, 2753889, 19741643.
-
(2009)
Nature Biotechnology
, vol.27
, Issue.9
, pp. 829-837
-
-
Wang, K.1
Saito, M.2
Bisikirska, B.C.3
Alvarez, M.J.4
Lim, W.K.5
Rajbhandari, P.6
Shen, Q.7
Nemenman, I.8
Basso, K.9
Margolin, A.A.10
Klein, U.11
Dalla-Favera, R.12
Califano, A.13
-
14
-
-
36448946146
-
Improved detection of overrepresentation of gene-ontology annotations with parent-child analysis
-
Grossmann S, Bauer S, Robinson PN, Vingron M. Improved detection of overrepresentation of gene-ontology annotations with parent-child analysis. Bioinformatics 2007,
-
(2007)
Bioinformatics
-
-
Grossmann, S.1
Bauer, S.2
Robinson, P.N.3
Vingron, M.4
-
15
-
-
77954376945
-
GOing Bayesian: model-based gene set analysis of genome-scale data
-
10.1093/nar/gkq045, 2887944, 20172960
-
Bauer S, Gagneur J, Robinson PN. GOing Bayesian: model-based gene set analysis of genome-scale data. Nucleic acids research 2010, 38(11):3523-3532. 10.1093/nar/gkq045, 2887944, 20172960.
-
(2010)
Nucleic acids research
, vol.38
, Issue.11
, pp. 3523-3532
-
-
Bauer, S.1
Gagneur, J.2
Robinson, P.N.3
-
16
-
-
55049103705
-
A probabilistic generative model for GO enrichment analysis
-
2553574, 18676451
-
Lu Y, Rosenfeld R, Simon I, Nau GJ, Bar-Joseph Z. A probabilistic generative model for GO enrichment analysis. Nucl. Acids Res 2008, 36(17):e109+. 2553574, 18676451.
-
(2008)
Nucl. Acids Res
, vol.36
, Issue.17
-
-
Lu, Y.1
Rosenfeld, R.2
Simon, I.3
Nau, G.J.4
Bar-Joseph, Z.5
-
17
-
-
4444346431
-
On the uniform generation of random graphs with prescribed degree sequences
-
Milo R, Kashtan N, Itzkovitz S, Newman M, Alon U. On the uniform generation of random graphs with prescribed degree sequences. Arxiv preprint cond-mat/0312028 2003,
-
(2003)
Arxiv preprint cond-mat/0312028
-
-
Milo, R.1
Kashtan, N.2
Itzkovitz, S.3
Newman, M.4
Alon, U.5
-
18
-
-
0034069495
-
Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium
-
10.1038/75556, 3037419, 10802651
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-9. 10.1038/75556, 3037419, 10802651.
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
Harris, M.A.11
Hill, D.P.12
Kasarskis, A.13
Lewis, S.14
Matese, J.C.15
Richardson, J.E.16
Ringwald, M.17
Rubin, G.M.18
Sherlock, G.19
-
19
-
-
38049129809
-
A context-specific network of protein-DNA and protein-protein interactions reveals new regulatory motifs in human B cells
-
Berlin, Heidelberg: Springer-Verlag
-
Lefebvre C, Lim WK, Basso K, Favera RD, Califano A. A context-specific network of protein-DNA and protein-protein interactions reveals new regulatory motifs in human B cells. Proceedings of the Joint 2006 satellite conference on Systems Biology and Computational Proteomics 2007, 42-56. Berlin, Heidelberg: Springer-Verlag.
-
(2007)
Proceedings of the Joint 2006 satellite conference on Systems Biology and Computational Proteomics
, pp. 42-56
-
-
Lefebvre, C.1
Lim, W.K.2
Basso, K.3
Favera, R.D.4
Califano, A.5
-
20
-
-
27344435774
-
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian A, Tamayo P, Mootha V, Mukherjee S, Ebert B, Gillette M, Paulovich A, Pomeroy S, Golub T, Lander E, Mesirov J. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 2005,
-
(2005)
Proc Natl Acad Sci U S A
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.3
Mukherjee, S.4
Ebert, B.5
Gillette, M.6
Paulovich, A.7
Pomeroy, S.8
Golub, T.9
Lander, E.10
Mesirov, J.11
-
21
-
-
78649665276
-
A comparative study of genome-wide transcriptional profiles of primary hepatocytes in collagen sandwich and monolayer cultures
-
Kim Y, Lasher CD, Milford LM, Murali TM, Rajagopalan P. A comparative study of genome-wide transcriptional profiles of primary hepatocytes in collagen sandwich and monolayer cultures. Tissue Eng Part C Methods 2010,
-
(2010)
Tissue Eng Part C Methods
-
-
Kim, Y.1
Lasher, C.D.2
Milford, L.M.3
Murali, T.M.4
Rajagopalan, P.5
-
22
-
-
34147217542
-
Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map
-
10.1038/nature05649, 17314980
-
Collins SR, Miller KM, Maas NL, Roguev A, Fillingham J, Chu CS, Schuldiner M, Gebbia M, Recht J, Shales M, Ding H, Xu H, Han J, Ingvarsdottir K, Cheng B, Andrews B, Boone C, Berger SL, Hieter P, Zhang Z, Brown GW, Ingles CJ, Emili A, Allis CD, Toczyski DP, Weissman JS, Greenblatt JF, Krogan NJ. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 2007, 446(7137):806-810. 10.1038/nature05649, 17314980.
-
(2007)
Nature
, vol.446
, Issue.7137
, pp. 806-810
-
-
Collins, S.R.1
Miller, K.M.2
Maas, N.L.3
Roguev, A.4
Fillingham, J.5
Chu, C.S.6
Schuldiner, M.7
Gebbia, M.8
Recht, J.9
Shales, M.10
Ding, H.11
Xu, H.12
Han, J.13
Ingvarsdottir, K.14
Cheng, B.15
Andrews, B.16
Boone, C.17
Berger, S.L.18
Hieter, P.19
Zhang, Z.20
Brown, G.W.21
Ingles, C.J.22
Emili, A.23
Allis, C.D.24
Toczyski, D.P.25
Weissman, J.S.26
Greenblatt, J.F.27
Krogan, N.J.28
more..
-
23
-
-
78651328883
-
The BioGRID Interaction Database: 2011 update
-
3013707, 21071413, Database issue
-
Stark C, Breitkreutz BJJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang X, Shi X, Reguly T, Rust JM, Winter A, Dolinski K, Tyers M. The BioGRID Interaction Database: 2011 update. Nucleic Acids Research 2011, 39(Database issue):D698-D704. 3013707, 21071413.
-
(2011)
Nucleic Acids Research
, vol.39
-
-
Stark, C.1
Breitkreutz, B.J.J.2
Chatr-Aryamontri, A.3
Boucher, L.4
Oughtred, R.5
Livstone, M.S.6
Nixon, J.7
Van Auken, K.8
Wang, X.9
Shi, X.10
Reguly, T.11
Rust, J.M.12
Winter, A.13
Dolinski, K.14
Tyers, M.15
-
24
-
-
52949127381
-
The Synergizer service for translating gene, protein and other biological identifiers
-
10.1093/bioinformatics/btn424, 2553440, 18697767
-
Berriz GF, Roth FP. The Synergizer service for translating gene, protein and other biological identifiers. Bioinformatics 2008, 24(19):2272-2273. 10.1093/bioinformatics/btn424, 2553440, 18697767.
-
(2008)
Bioinformatics
, vol.24
, Issue.19
, pp. 2272-2273
-
-
Berriz, G.F.1
Roth, F.P.2
-
25
-
-
0242490780
-
Cytoscape: a software environment for integrated models of biomolecular interaction networks
-
10.1101/gr.1239303, 403769, 14597658
-
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13(11):2498-504. 10.1101/gr.1239303, 403769, 14597658.
-
(2003)
Genome Res
, vol.13
, Issue.11
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
-
26
-
-
53349103292
-
Modelling Myc inhibition as a cancer therapy
-
10.1038/nature07260, 18716624
-
Soucek L, Whitfield J, Martins CP, Finch AJ, Murphy DJ, Sodir NM, Karnezis AN, Swigart LB, Nasi S, Evan GI. Modelling Myc inhibition as a cancer therapy. Nature 2008, 455(7213):679-683. 10.1038/nature07260, 18716624.
-
(2008)
Nature
, vol.455
, Issue.7213
, pp. 679-683
-
-
Soucek, L.1
Whitfield, J.2
Martins, C.P.3
Finch, A.J.4
Murphy, D.J.5
Sodir, N.M.6
Karnezis, A.N.7
Swigart, L.B.8
Nasi, S.9
Evan, G.I.10
-
27
-
-
79251560010
-
The role of STAT5 in the development, function, and transformation of B and T lymphocytes
-
10.1111/j.1749-6632.2010.05907.x, 21276004
-
Heltemes-Harris LM, Willette MJL, Vang KB, Farrar MA. The role of STAT5 in the development, function, and transformation of B and T lymphocytes. Annals of the New York Academy of Sciences 2011, 1217:18-31. 10.1111/j.1749-6632.2010.05907.x, 21276004.
-
(2011)
Annals of the New York Academy of Sciences
, vol.1217
, pp. 18-31
-
-
Heltemes-Harris, L.M.1
Willette, M.J.L.2
Vang, K.B.3
Farrar, M.A.4
-
29
-
-
78651324347
-
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
-
3013807, 21045058, Database issue
-
Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering C. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Research 2011, 39(Database issue):D561-D568. 3013807, 21045058.
-
(2011)
Nucleic Acids Research
, vol.39
-
-
Szklarczyk, D.1
Franceschini, A.2
Kuhn, M.3
Simonovic, M.4
Roth, A.5
Minguez, P.6
Doerks, T.7
Stark, M.8
Muller, J.9
Bork, P.10
Jensen, L.J.11
von Mering, C.12
-
30
-
-
33644872577
-
Bioinformatics and computational biology solutions using R and bioconductor
-
Springer
-
Smyth GK. Bioinformatics and computational biology solutions using R and bioconductor. chap Limma: linear models for microarray data 2005, 397-420. Springer.
-
(2005)
chap Limma: linear models for microarray data
, pp. 397-420
-
-
Smyth, G.K.1
-
31
-
-
77951972600
-
BioNet: an R-Package for the functional analysis of biological networks
-
10.1093/bioinformatics/btq089, 20189939
-
Beisser D, Klau GW, Dandekar T, Muller T, Dittrich MT. BioNet: an R-Package for the functional analysis of biological networks. Bioinformatics 2010, 26(8):1129-30. 10.1093/bioinformatics/btq089, 20189939.
-
(2010)
Bioinformatics
, vol.26
, Issue.8
, pp. 1129-1130
-
-
Beisser, D.1
Klau, G.W.2
Dandekar, T.3
Muller, T.4
Dittrich, M.T.5
-
32
-
-
79955566080
-
Signaling pathways that control cell migration: models and analysis
-
10.1002/wsbm.110, 3052860, 21305705
-
Welf ES, Haugh JM. Signaling pathways that control cell migration: models and analysis. Wiley interdisciplinary reviews. Systems biology and medicine 2011, 3(2):231-240. 10.1002/wsbm.110, 3052860, 21305705.
-
(2011)
Wiley interdisciplinary reviews. Systems biology and medicine
, vol.3
, Issue.2
, pp. 231-240
-
-
Welf, E.S.1
Haugh, J.M.2
-
33
-
-
25844484820
-
Thinking outside the cell: proteases regulate hepatocyte division
-
10.1016/j.tcb.2005.08.009, 16150595
-
Mohammed FF, Khokha R. Thinking outside the cell: proteases regulate hepatocyte division. Trends in Cell Biology 2005, 15(10):555-563. 10.1016/j.tcb.2005.08.009, 16150595.
-
(2005)
Trends in Cell Biology
, vol.15
, Issue.10
, pp. 555-563
-
-
Mohammed, F.F.1
Khokha, R.2
-
34
-
-
33847018050
-
Primary hepatocytes: current understanding of the regulation of metabolic enzymes and transporter proteins, and pharmaceutical practice for the use of hepatocytes in metabolism, enzyme induction, transporter, clearance, and hepatotoxicity studies
-
10.1080/03602530601093489, 17364884
-
Hewitt NJ, Gómez Lechón MJ, Houston JB, Hallifax D, Brown HS, Maurel P, Kenna JG, Gustavsson L, Lohmann C, Skonberg C, Guillouzo A, Tuschl G, Li AP, LeCluyse E, Groothuis GMM, Hengstler JG. Primary hepatocytes: current understanding of the regulation of metabolic enzymes and transporter proteins, and pharmaceutical practice for the use of hepatocytes in metabolism, enzyme induction, transporter, clearance, and hepatotoxicity studies. Drug Metabolism Reviews 2007, 39:159-234. 10.1080/03602530601093489, 17364884.
-
(2007)
Drug Metabolism Reviews
, vol.39
, pp. 159-234
-
-
Hewitt, N.J.1
Gómez Lechón, M.J.2
Houston, J.B.3
Hallifax, D.4
Brown, H.S.5
Maurel, P.6
Kenna, J.G.7
Gustavsson, L.8
Lohmann, C.9
Skonberg, C.10
Guillouzo, A.11
Tuschl, G.12
Li, A.P.13
LeCluyse, E.14
Groothuis, G.M.M.15
Hengstler, J.G.16
-
35
-
-
15844429977
-
Superoxide dismutase activity is essential for stationary phase survival in Saccharomyces cerevisiae. Mitochondrial production of toxic oxygen species in vivo
-
10.1074/jbc.271.21.12275, 8647826
-
Longo VD, Gralla EB, Valentine JS. Superoxide dismutase activity is essential for stationary phase survival in Saccharomyces cerevisiae. Mitochondrial production of toxic oxygen species in vivo. The Journal of Biological Chemistry 1996, 271(21):12275-12280. 10.1074/jbc.271.21.12275, 8647826.
-
(1996)
The Journal of Biological Chemistry
, vol.271
, Issue.21
, pp. 12275-12280
-
-
Longo, V.D.1
Gralla, E.B.2
Valentine, J.S.3
|