-
1
-
-
0035338343
-
Risks in new drug development: Approval success rates for investigational drugs
-
DiMasi JA: Risks in new drug development: Approval success rates for investigational drugs. Clin Pharmacol Ther (2001) 69(5):297-307.
-
(2001)
Clin Pharmacol Ther
, vol.69
, Issue.5
, pp. 297-307
-
-
DiMasi, J.A.1
-
3
-
-
0028806048
-
Quantitative monitoring of gene expression patterns with a complementary DNA microarray
-
Schena M, Shalon D, Davis RW, Brown PO: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science (1995) 270(5235):467-470.
-
(1995)
Science
, vol.270
, Issue.5235
, pp. 467-470
-
-
Schena, M.1
Shalon, D.2
Davis, R.W.3
Brown, P.O.4
-
4
-
-
10544256600
-
Expression monitoring by hybridization to high-density oligonucleotide arrays
-
Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL: Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol (1996) 14(13):1675-1680.
-
(1996)
Nat Biotechnol
, vol.14
, Issue.13
, pp. 1675-1680
-
-
Lockhart, D.J.1
Dong, H.2
Byrne, M.C.3
Follettie, M.T.4
Gallo, M.V.5
Chee, M.S.6
Mittmann, M.7
Wang, C.8
Kobayashi, M.9
Horton, H.10
Brown, E.L.11
-
5
-
-
0037434980
-
From genomics to proteomics
-
Tyers M, Mann M: From genomics to proteomics. Nature (2003) 422(6928):193-197.
-
(2003)
Nature
, vol.422
, Issue.6928
, pp. 193-197
-
-
Tyers, M.1
Mann, M.2
-
6
-
-
0032875697
-
Quantitative analysis of complex protein mixtures using isotope-coded affinity tags
-
Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R: Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol (1999) 17(10):994-999. Description of a method for quantifying proteins using mass spectrometry.
-
(1999)
Nat Biotechnol
, vol.17
, Issue.10
, pp. 994-999
-
-
Gygi, S.P.1
Rist, B.2
Gerber, S.A.3
Turecek, F.4
Gelb, M.H.5
Aebersold, R.6
-
7
-
-
4043141477
-
Quantitative cancer proteomics: Stable isotope labeling with amino acids in cell culture (SILAC) as a tool for prostate cancer research
-
Everley PA, Krijgsveld J, Zetter BR, Gygi SP: Quantitative cancer proteomics: Stable isotope labeling with amino acids in cell culture (SILAC) as a tool for prostate cancer research. Mol Cell Proteomics (2004) 3(7):729-735.
-
(2004)
Mol Cell Proteomics
, vol.3
, Issue.7
, pp. 729-735
-
-
Everley, P.A.1
Krijgsveld, J.2
Zetter, B.R.3
Gygi, S.P.4
-
8
-
-
10744233766
-
Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards
-
Wang W, Zhou H, Lin H, Roy S, Shaler TA, Hill LR, Norton S, Kumar P, Anderle M, Becker CH: Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal Chem (2003) 75(18):4818-4826.
-
(2003)
Anal Chem
, vol.75
, Issue.18
, pp. 4818-4826
-
-
Wang, W.1
Zhou, H.2
Lin, H.3
Roy, S.4
Shaler, T.A.5
Hill, L.R.6
Norton, S.7
Kumar, P.8
Anderle, M.9
Becker, C.H.10
-
9
-
-
12244294247
-
System-based proteomic analysis of the interferon response in human liver cells
-
Van W, Lee H, Yi EC, Reiss D, Shannon P, Kwieciszewski BK, Coito C, Li XJ, Keller A, Eng J, Galitski T et al: System-based proteomic analysis of the interferon response in human liver cells. Genome Biol (2004) 5(8):R54.
-
(2004)
Genome Biol
, vol.5
, Issue.8
-
-
Van, W.1
Lee, H.2
Yi, E.C.3
Reiss, D.4
Shannon, P.5
Kwieciszewski, B.K.6
Coito, C.7
Li, X.J.8
Keller, A.9
Eng, J.10
Galitski, T.11
-
10
-
-
20144368638
-
Integrated genomic and proteomic analyses of gene expression in mammalian cells
-
Tian Q, Stepaniants SB, Mao M, Weng L, Feetham MC, Doyle MJ, Yi EC, Dai H, Thorsson V, Eng J, Goodlett D et al: Integrated genomic and proteomic analyses of gene expression in mammalian cells. Mol Cell Proteomics (2004) 3(10):960-969 Describes a large-scale comparison of microarray and proteomics datasets in mouse and human cell lines, and demonstrates that the differential expression of mRNA captures only 40% of the variation of protein expression in mammalian cells.
-
(2004)
Mol Cell Proteomics
, vol.3
, Issue.10
, pp. 960-969
-
-
Tian, Q.1
Stepaniants, S.B.2
Mao, M.3
Weng, L.4
Feetham, M.C.5
Doyle, M.J.6
Yi, E.C.7
Dai, H.8
Thorsson, V.9
Eng, J.10
Goodlett, D.11
-
11
-
-
0042925411
-
Profiling receptor tyrosine kinase activation by using Ab microarrays
-
Nielsen UB, Cardone MH, Sinskey AJ, MacBeath G, Sorger PK: Profiling receptor tyrosine kinase activation by using Ab microarrays. Proc Natl Acad Sci USA (2003) 100(16):9330-9335.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, Issue.16
, pp. 9330-9335
-
-
Nielsen, U.B.1
Cardone, M.H.2
Sinskey, A.J.3
MacBeath, G.4
Sorger, P.K.5
-
13
-
-
10944246119
-
Localization of organelle proteins by isotope tagging (LOPIT)
-
Dunkley TP, Watson R, Griffin JL, Dupree P, Lilley KS: Localization of organelle proteins by isotope tagging (LOPIT). Mol Cell Proteomics (2004) 3(11):1128-1134. Describes a method that allows subcellular localization of proteins.
-
(2004)
Mol Cell Proteomics
, vol.3
, Issue.11
, pp. 1128-1134
-
-
Dunkley, T.P.1
Watson, R.2
Griffin, J.L.3
Dupree, P.4
Lilley, K.S.5
-
14
-
-
3242775565
-
PROCEED: A proteomic method for analysing plasma membrane proteins in living mammalian cells
-
Bledi Y, Inberg A, Linial M: PROCEED: A proteomic method for analysing plasma membrane proteins in living mammalian cells. Brief Funct Genomic Proteomic (2003) 2(3):254-265.
-
(2003)
Brief Funct Genomic Proteomic
, vol.2
, Issue.3
, pp. 254-265
-
-
Bledi, Y.1
Inberg, A.2
Linial, M.3
-
15
-
-
3042654830
-
Protein expression profiling arrays: Tools for the multiplexed high-throughput analysis of proteins
-
Sydor JR, Nock S: Protein expression profiling arrays: Tools for the multiplexed high-throughput analysis of proteins. Proteome Sci (2003) 1(1):3. http://www.proteomesci.com/content/1/1/3 Review discussing the challenges of building protein arrays.
-
(2003)
Proteome Sci
, vol.1
, Issue.1
, pp. 3
-
-
Sydor, J.R.1
Nock, S.2
-
16
-
-
2942527049
-
Lipomic profiling in drug discovery, development and clinical trial evaluation
-
Watkins SM: Lipomic profiling in drug discovery, development and clinical trial evaluation. Curr Opin Drug Discovery Dev (2004) 7(1):112-117.
-
(2004)
Curr Opin Drug Discovery Dev
, vol.7
, Issue.1
, pp. 112-117
-
-
Watkins, S.M.1
-
17
-
-
0037050020
-
Protein complexes take the bait
-
Kumar A, Snyder M: Protein complexes take the bait. Nature (2002) 415(6868):123-124.
-
(2002)
Nature
, vol.415
, Issue.6868
, pp. 123-124
-
-
Kumar, A.1
Snyder, M.2
-
18
-
-
0032828715
-
A generic protein purification method for protein complex characterization and proteome exploration
-
Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Seraphin B: A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol (1999) 17(10):1030-1032.
-
(1999)
Nat Biotechnol
, vol.17
, Issue.10
, pp. 1030-1032
-
-
Rigaut, G.1
Shevchenko, A.2
Rutz, B.3
Wilm, M.4
Mann, M.5
Seraphin, B.6
-
19
-
-
0035252675
-
Protein arrays and microarrays
-
Zhu H, Snyder M: Protein arrays and microarrays. Curr Opin Chem Biol (2001) 5(1):40-45.
-
(2001)
Curr Opin Chem Biol
, vol.5
, Issue.1
, pp. 40-45
-
-
Zhu, H.1
Snyder, M.2
-
20
-
-
0242354926
-
Parallel determination of multiple protein metabolite interactions using cell extract, protein microarrays and mass spectrometric detection
-
Morozov VN, Morozova TY, Johnson KL, Naylor S: Parallel determination of multiple protein metabolite interactions using cell extract, protein microarrays and mass spectrometric detection. Rapid Commun Mass Spectrom (2003) 17(21):2430-2438.
-
(2003)
Rapid Commun Mass Spectrom
, vol.17
, Issue.21
, pp. 2430-2438
-
-
Morozov, V.N.1
Morozova, T.Y.2
Johnson, K.L.3
Naylor, S.4
-
21
-
-
3042790024
-
Enthalpy arrays
-
Torres FE, Kuhn P, De Bruyker D, Bell AG, Wolkin MV, Peelers E, Williamson JR, Anderson GB, Schmitz GP, Recht MI, Schweizer S et al: Enthalpy arrays. Proc Natl Acad Sci USA (2004) 101(26):9517-9522. Describes a novel technology for identifying protein interactions.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, Issue.26
, pp. 9517-9522
-
-
Torres, F.E.1
Kuhn, P.2
De Bruyker, D.3
Bell, A.G.4
Wolkin, M.V.5
Peelers, E.6
Williamson, J.R.7
Anderson, G.B.8
Schmitz, G.P.9
Recht, M.I.10
Schweizer, S.11
-
22
-
-
3943087720
-
Analyzing cellular biochemistry in terms of molecular networks
-
Xia Y, Yu H, Jansen R, Seringhaus M, Baxters, Greenbaum D, Zhao H, Gerstein M: Analyzing cellular biochemistry in terms of molecular networks. Annu Rev Biochem (2004) 73:1051-1087. An excellent review of current approaches for identifying signaling network components and component interactions.
-
(2004)
Annu Rev Biochem
, vol.73
, pp. 1051-1087
-
-
Xia, Y.1
Yu, H.2
Jansen, R.3
Seringhaus, M.4
Baxters5
Greenbaum, D.6
Zhao, H.7
Gerstein, M.8
-
23
-
-
0033974688
-
Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins
-
Ito T, Tashiro K, Muta S, Ozawa R, Chiba T, Nishizawa M, Yamamoto K, Kuhara S, Sakaki Y: Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc Natl Acad Sci USA (2000) 97(3):1143-1147.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, Issue.3
, pp. 1143-1147
-
-
Ito, T.1
Tashiro, K.2
Muta, S.3
Ozawa, R.4
Chiba, T.5
Nishizawa, M.6
Yamamoto, K.7
Kuhara, S.8
Sakaki, Y.9
-
24
-
-
0034628508
-
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
-
Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A et al: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature (2000) 403(6770):623-627.
-
(2000)
Nature
, vol.403
, Issue.6770
, pp. 623-627
-
-
Uetz, P.1
Giot, L.2
Cagney, G.3
Mansfield, T.A.4
Judson, R.S.5
Knight, J.R.6
Lockshon, D.7
Narayan, V.8
Srinivasan, M.9
Pochart, P.10
Qureshi-Emili, A.11
-
25
-
-
1842580761
-
Functional and topological characterization of protein interaction networks
-
Yook SH, Oltvai ZN, Barabasi AL: Functional and topological characterization of protein interaction networks. Proteomics (2004) 4(4):928-942.
-
(2004)
Proteomics
, vol.4
, Issue.4
, pp. 928-942
-
-
Yook, S.H.1
Oltvai, Z.N.2
Barabasi, A.L.3
-
26
-
-
0035836765
-
A comprehensive two-hybrid analysis to explore the yeast protein interactome
-
Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y: A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA (2001) 98(8):4569-4574.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, Issue.8
, pp. 4569-4574
-
-
Ito, T.1
Chiba, T.2
Ozawa, R.3
Yoshida, M.4
Hattori, M.5
Sakaki, Y.6
-
27
-
-
4444371652
-
Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics
-
Blagoev B, Ong SE, Kratchmarova I, Mann M: Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat Biotechnol (2004) 22(9):1139-1145.
-
(2004)
Nat Biotechnol
, vol.22
, Issue.9
, pp. 1139-1145
-
-
Blagoev, B.1
Ong, S.E.2
Kratchmarova, I.3
Mann, M.4
-
28
-
-
0032441150
-
Cluster analysis and display of genome-wide expression patterns
-
Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA (1998) 95(25):14863-14868.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, Issue.25
, pp. 14863-14868
-
-
Eisen, M.B.1
Spellman, P.T.2
Brown, P.O.3
Botstein, D.4
-
29
-
-
0034568109
-
'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns
-
RESEARCH0003
-
Hastie T, Tibshirani R, Eisen MB, Alizadeh A, Levy R, Staudt L, Chan WC, Botstein D, Brown P: 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns. Genome Biol (2000) 1(2):RESEARCH0003.
-
(2000)
Genome Biol
, vol.1
, Issue.2
-
-
Hastie, T.1
Tibshirani, R.2
Eisen, M.B.3
Alizadeh, A.4
Levy, R.5
Staudt, L.6
Chan, W.C.7
Botstein, D.8
Brown, P.9
-
30
-
-
0347473810
-
Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways
-
Parsons AB, Brost RL, Ding H, Li Z, Zhang C, Sheikh B, Brown GW, Kane PM, Hughes TR, Boone C: Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways. Nat Biotechnol (2004) 22(1):62-69. Description of an indirect approach to exploring signaling networks, which integrates chemical-genetic and genetic interaction data from yeast to identify pathways or proteins targeted by compounds.
-
(2004)
Nat Biotechnol
, vol.22
, Issue.1
, pp. 62-69
-
-
Parsons, A.B.1
Brost, R.L.2
Ding, H.3
Li, Z.4
Zhang, C.5
Sheikh, B.6
Brown, G.W.7
Kane, P.M.8
Hughes, T.R.9
Boone, C.10
-
31
-
-
0003684449
-
-
Springer-Verlag, New York, NY, USA
-
Hastie T, Tibshirani R, Friedman JH: The Elements of Statistical Learning: Data Mining, Inference and Prediction. Springer-Verlag, New York, NY, USA (2001). An excellent reference for data mining methods used for analysis of biological data.
-
(2001)
The Elements of Statistical Learning: Data Mining, Inference and Prediction
-
-
Hastie, T.1
Tibshirani, R.2
Friedman, J.H.3
-
32
-
-
19344375744
-
Semi-supervised methods to predict patient survival from gene expression data
-
Bair E, Tibshirani R: Semi-supervised methods to predict patient survival from gene expression data. PLoS Biol (2004) 2(4):E108.
-
(2004)
PLoS Biol
, vol.2
, Issue.4
-
-
Bair, E.1
Tibshirani, R.2
-
34
-
-
0037142053
-
The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma
-
Rosenwald A, Wright G, Chan WC, Connors JM, Campo E, Fisher RI, Gascoyne RD, Muller-Hermelink HK, Smeland EB, Giltnane JM, Hurt EM et al: The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N Engl J Med (2002) 346(25):1937-1947.
-
(2002)
N Engl J Med
, vol.346
, Issue.25
, pp. 1937-1947
-
-
Rosenwald, A.1
Wright, G.2
Chan, W.C.3
Connors, J.M.4
Campo, E.5
Fisher, R.I.6
Gascoyne, R.D.7
Muller-Hermelink, H.K.8
Smeland, E.B.9
Giltnane, J.M.10
Hurt, E.M.11
-
35
-
-
3042655539
-
Cell-type-specific responses to chemotherapeutics in breast cancer
-
Troester MA, Hoadley KA, Sorlie T, Herbert BS, Borresen-Dale AL, Lonning PE, Shay JW, Kaufmann WK, Perou CM: Cell-type-specific responses to chemotherapeutics in breast cancer. Cancer Res (2004) 64(12):4218-4226.
-
(2004)
Cancer Res
, vol.64
, Issue.12
, pp. 4218-4226
-
-
Troester, M.A.1
Hoadley, K.A.2
Sorlie, T.3
Herbert, B.S.4
Borresen-Dale, A.L.5
Lonning, P.E.6
Shay, J.W.7
Kaufmann, W.K.8
Perou, C.M.9
-
36
-
-
0031616241
-
REVEAL, a general reverse engineering algorithm for inference of genetic network architectures
-
Liang S, Fuhrman S, Somogyi R: REVEAL, a general reverse engineering algorithm for inference of genetic network architectures. Pacific Symp Biocomput (1998) 3:18-29. Description of the development and analysis of an algorithm for causal inference based on the correlation measure of mutual information.
-
(1998)
Pacific Symp Biocomput
, vol.3
, pp. 18-29
-
-
Liang, S.1
Fuhrman, S.2
Somogyi, R.3
-
37
-
-
0033642067
-
Discovery of regulatory interactions through perturbation: Inference and experimental design
-
Ideker TE, Thorsson V, Karp RM: Discovery of regulatory interactions through perturbation: Inference and experimental design. Pacific Symp Biocomput (2000) 5:305-316. Description of the perturbation approach for building networks.
-
(2000)
Pacific Symp Biocomput
, vol.5
, pp. 305-316
-
-
Ideker, T.E.1
Thorsson, V.2
Karp, R.M.3
-
38
-
-
0032616683
-
Identification of genetic networks from a small number of gene expression patterns under the Boolean network model
-
Akutsu T, Miyano S, Kuhara S: Identification of genetic networks from a small number of gene expression patterns under the Boolean network model. Pacific Symp Biocomput (1999) 4:17-28. Mathematical analysis of the number of gene expression patterns required for the identification of a genetic network under the Boolean network model.
-
(1999)
Pacific Symp Biocomput
, vol.4
, pp. 17-28
-
-
Akutsu, T.1
Miyano, S.2
Kuhara, S.3
-
39
-
-
0036184629
-
Probabilistic Boolean networks: A rule-based uncertainty model for gene regulatory networks
-
Shmulevich I, Dougherty ER, Kim S, Zhang W: Probabilistic Boolean networks: A rule-based uncertainty model for gene regulatory networks. Bioinformatics (2002) 18(2):261-274.
-
(2002)
Bioinformatics
, vol.18
, Issue.2
, pp. 261-274
-
-
Shmulevich, I.1
Dougherty, E.R.2
Kim, S.3
Zhang, W.4
-
40
-
-
0033707946
-
Using Bayesian networks to analyze expression data
-
Friedman N, Linial M, Nachman I, Pe'er D: Using Bayesian networks to analyze expression data. J Comput Biol (2000) 7(3-4):601-620. Method for recovering gene interactions from expression data using Bayesian networks learning tools.
-
(2000)
J Comput Biol
, vol.7
, Issue.3-4
, pp. 601-620
-
-
Friedman, N.1
Linial, M.2
Nachman, I.3
Pe'er, D.4
-
41
-
-
3242875300
-
Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks
-
Imoto S, Higuchi T, Goto T, Tashiro K, Kuhara S, Miyano S: Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks. J Bioinform Comput Biol (2004) 2(1):77-98. Description of a Bayesian network framework which incorporates gene expression, protein-DNA interaction, protein-protein interaction, binding site and literature data to model cell networks in yeast.
-
(2004)
J Bioinform Comput Biol
, vol.2
, Issue.1
, pp. 77-98
-
-
Imoto, S.1
Higuchi, T.2
Goto, T.3
Tashiro, K.4
Kuhara, S.5
Miyano, S.6
-
42
-
-
0142052944
-
A Bayesian networks approach for predicting protein-protein interactions from genomic data
-
Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M: A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 302(5644):449-453.
-
(2003)
Science
, vol.302
, Issue.5644
, pp. 449-453
-
-
Jansen, R.1
Yu, H.2
Greenbaum, D.3
Kluger, Y.4
Krogan, N.J.5
Chung, S.6
Emili, A.7
Snyder, M.8
Greenblatt, J.F.9
Gerstein, M.10
-
43
-
-
0038048325
-
Inferring genetic networks and identifying compound mode of action via expression profiling
-
Gardner TS, di Bernardo D, Lorenz D, Collins JJ: Inferring genetic networks and identifying compound mode of action via expression profiling. Science (2003) 301(5629):102-105. Description of an approach using transcriptional perturbations to build a model of a subnetwork of the SOS pathway in bacteria and its application to study network properties and identify molecular targets of drugs.
-
(2003)
Science
, vol.301
, Issue.5629
, pp. 102-105
-
-
Gardner, T.S.1
Di Bernardo, D.2
Lorenz, D.3
Collins, J.J.4
-
44
-
-
4444356634
-
Use of gene networks for identifying and validating drug targets
-
Imoto S, Savoie CJ, Aburatani S, Kim S, Tashiro K, Kuhara S, Miyano S: Use of gene networks for identifying and validating drug targets. J Bioinform Comput Biol (2003) 1(3):459-474. Description of a method for identifying drug targets using gene disruption and drug response gene expression data combined with Bayesian network formalism, including a demonstration of application of the strategy to drug discovery using yeast gene expression data.
-
(2003)
J Bioinform Comput Biol
, vol.1
, Issue.3
, pp. 459-474
-
-
Imoto, S.1
Savoie, C.J.2
Aburatani, S.3
Kim, S.4
Tashiro, K.5
Kuhara, S.6
Miyano, S.7
-
45
-
-
3042668008
-
Modeling cell signaling networks
-
Eungdamrong NJ, Iyengar R: Modeling cell signaling networks. Biol Cell (2004) 96(5):355-362. Discussion of the different mathematical approaches employed to model signaling networks.
-
(2004)
Biol Cell
, vol.96
, Issue.5
, pp. 355-362
-
-
Eungdamrong, N.J.1
Iyengar, R.2
-
46
-
-
2942514591
-
Biochemical Network Stochastic Simulator (BioNetS): Software for stochastic modeling of biochemical networks
-
Adalsteinsson D, McMillen D, Elston TC: Biochemical Network Stochastic Simulator (BioNetS): Software for stochastic modeling of biochemical networks. BMC Bioinformatics (2004) 5(1):24.
-
(2004)
BMC Bioinformatics
, vol.5
, Issue.1
, pp. 24
-
-
Adalsteinsson, D.1
McMillen, D.2
Elston, T.C.3
-
47
-
-
2342469914
-
Stochastic model of protein-protein interaction: Why signaling proteins need to be colocalized
-
Batada NN, Shepp LA, Siegmund DO: Stochastic model of protein-protein interaction: Why signaling proteins need to be colocalized. Proc Natl Acad Sci USA (2004) 101(17):6445-6449.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, Issue.17
, pp. 6445-6449
-
-
Batada, N.N.1
Shepp, L.A.2
Siegmund, D.O.3
-
48
-
-
0041843750
-
An integrated model of epidermal growth factor receptor trafficking and signal transduction
-
Resat H, Ewald JA, Dixon DA, Wiley HS: An integrated model of epidermal growth factor receptor trafficking and signal transduction. Biophys J (2003) 85(2):730-743.
-
(2003)
Biophys J
, vol.85
, Issue.2
, pp. 730-743
-
-
Resat, H.1
Ewald, J.A.2
Dixon, D.A.3
Wiley, H.S.4
-
49
-
-
0036212767
-
Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors
-
Schoeberl B, Eichler-Jonsson C, Gilles ED, Muller G: Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nat Biotechnol (2002) 20(4):370-375.
-
(2002)
Nat Biotechnol
, vol.20
, Issue.4
, pp. 370-375
-
-
Schoeberl, B.1
Eichler-Jonsson, C.2
Gilles, E.D.3
Muller, G.4
-
50
-
-
12144289400
-
A physical and functional map of the human TNFα/NFκB signal transduction pathway
-
Bouwmeester T, Bauch A, Ruffner H, Angrand PO, Bergamini G, Croughton K, Cruciat C, Eberhard D, Gagneur J, Ghidelli S, Hopf C et al: A physical and functional map of the human TNFα/NFκB signal transduction pathway. Nat Cell Biol (2004) 6(2):97-105. Combining protein pull-down, LC/MS and directed functional perturbation studies using RNA interference, the authors were able to generate a protein connectivity map of the TNFα/NFκB signal pathway in HEK293 cells, a human embryonic kidney cell line.
-
(2004)
Nat Cell Biol
, vol.6
, Issue.2
, pp. 97-105
-
-
Bouwmeester, T.1
Bauch, A.2
Ruffner, H.3
Angrand, P.O.4
Bergamini, G.5
Croughton, K.6
Cruciat, C.7
Eberhard, D.8
Gagneur, J.9
Ghidelli, S.10
Hopf, C.11
-
51
-
-
2942576105
-
Data-driven computer simulation of human cancer cell
-
Christopher R, Dhiman A, Fox J, Gendelman R, Haberitcher T, Kagle D, Spizz G, Khalil IG, Hill C: Data-driven computer simulation of human cancer cell. Ann NY Acad Sci (2004) 1020:132-153. Description of the building of a graphical network model of a human colon cancer cell containing over 1000 genes and proteins and a simulation model that can be tested by 'virtual' knockdown experiments.
-
(2004)
Ann NY Acad Sci
, vol.1020
, pp. 132-153
-
-
Christopher, R.1
Dhiman, A.2
Fox, J.3
Gendelman, R.4
Haberitcher, T.5
Kagle, D.6
Spizz, G.7
Khalil, I.G.8
Hill, C.9
-
52
-
-
10744233471
-
Method for analyzing signaling networks in complex cellular systems
-
Plavec I, Sirenko O, Privat S, Wang Y, Dajee M, Melrose J, Nakao B, Hytopoulos E, Berg EL, Butcher EC: Method for analyzing signaling networks in complex cellular systems. Proc Natl Acad Sci USA (2004) 101(5):1223-1228. Outlines how the mapping of gene functions by overexpression in complex cell systems, combining data from multiple systems, car identify pathway cross-talk and feedback mechanisms.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, Issue.5
, pp. 1223-1228
-
-
Plavec, I.1
Sirenko, O.2
Privat, S.3
Wang, Y.4
Dajee, M.5
Melrose, J.6
Nakao, B.7
Hytopoulos, E.8
Berg, E.L.9
Butcher, E.C.10
-
53
-
-
4644264129
-
An integrative biology approach for analysis of drug action in models of human vascular inflammation
-
Kunkel EJ, Dea M, Ebens A, Hytopoulos E, Melrose J, Nguyen D, Ota KS, Plavec I, Wang Y, Watson SR, Butcher EC et al. An integrative biology approach for analysis of drug action in models of human vascular inflammation. FASEB J (2004) 18(11):1279-1281. Outlines how compound profiling in multiple complex cell systems can provide mechanism of actions and secondary target information.
-
(2004)
FASEB J
, vol.18
, Issue.11
, pp. 1279-1281
-
-
Kunkel, E.J.1
Dea, M.2
Ebens, A.3
Hytopoulos, E.4
Melrose, J.5
Nguyen, D.6
Ota, K.S.7
Plavec, I.8
Wang, Y.9
Watson, S.R.10
Butcher, E.C.11
-
54
-
-
4644326931
-
Genomic analysis of regulatory network dynamics reveals large topological changes
-
Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M: Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 431(7006):308-312. Description of an approach for statistical analysis of the dynamics of biological networks in yeast, in which unexpectedly large changes in the underlying network architecture were identified.
-
(2004)
Nature
, vol.431
, Issue.7006
, pp. 308-312
-
-
Luscombe, N.M.1
Babu, M.M.2
Yu, H.3
Snyder, M.4
Teichmann, S.A.5
Gerstein, M.6
-
55
-
-
2942544830
-
Tamoxifen resistance by a conformational arrest of the estrogen receptor α after PKA activation in breast cancer
-
Michalides R, Griekspoor A, Balkenende A, Verwoerd D, Janssen L, Jalink K, Floore A, Velds A, van't Veer L, Neefies J: Tamoxifen resistance by a conformational arrest of the estrogen receptor α after PKA activation in breast cancer. Cancer Cell (2004) 5(6):597-605.
-
(2004)
Cancer Cell
, vol.5
, Issue.6
, pp. 597-605
-
-
Michalides, R.1
Griekspoor, A.2
Balkenende, A.3
Verwoerd, D.4
Janssen, L.5
Jalink, K.6
Floore, A.7
Velds, A.8
Van't Veer, L.9
Neefies, J.10
|