-
1
-
-
0000122278
-
Statistical construction of chemical reaction mechanism from measured time-series
-
Arkin,A. and Ross,J. (1995) Statistical construction of chemical reaction mechanism from measured time-series. J. Phys. Chem. 99, 970-979.
-
(1995)
J. Phys. Chem.
, vol.99
, pp. 970-979
-
-
Arkin, A.1
Ross, J.2
-
2
-
-
0030848624
-
A test case of correlation metric construction of a reaction pathway from measurements
-
Arkin,A., Shen,P. and Ross,J. (1997) A test case of correlation metric construction of a reaction pathway from measurements. Science, 29, 1275-1279.
-
(1997)
Science
, vol.29
, pp. 1275-1279
-
-
Arkin, A.1
Shen, P.2
Ross, J.3
-
3
-
-
2942606066
-
Structure and evolution of transcriptional regulatory networks
-
Babu,M.M., Luscombe,N.M., Aravind,L., Gerstein,M. and Teichmann,S.A. (2004) Structure and evolution of transcriptional regulatory networks. Curr. Opin. Struct. Biol., 14, 283-291.
-
(2004)
Curr. Opin. Struct. Biol.
, vol.14
, pp. 283-291
-
-
Babu, M.M.1
Luscombe, N.M.2
Aravind, L.3
Gerstein, M.4
Teichmann, S.A.5
-
5
-
-
0038483826
-
Emergence of scaling in random networks
-
Barabasi,A.L. and Albert,R. (1999) Emergence of scaling in random networks. Science, 286, 509-512.
-
(1999)
Science
, vol.286
, pp. 509-512
-
-
Barabasi, A.L.1
Albert, R.2
-
6
-
-
0034212551
-
Engineering stability in gene networks by autoregulation
-
Becskei,A. and Serrano,L. (2000) Engineering stability in gene networks by autoregulation. Nature, 405, 590-593.
-
(2000)
Nature
, vol.405
, pp. 590-593
-
-
Becskei, A.1
Serrano, L.2
-
7
-
-
0033655775
-
Mutual information relevance networks: Functional genomic clustering using pairwise entropy measurements
-
Butte,A.J. and Kohane,I.S. (2000) Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac. Symp. Biocomput., 2000, 418-429.
-
(2000)
Pac. Symp. Biocomput.
, vol.2000
, pp. 418-429
-
-
Butte, A.J.1
Kohane, I.S.2
-
8
-
-
0034710924
-
Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks
-
Butte,A.J., Tamayo,P., Slonim,D., Golub,T.R. and Kohane,I.S. (2000) Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proc. Natl Acad. Sci. USA, 97, 12182-12186.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 12182-12186
-
-
Butte, A.J.1
Tamayo, P.2
Slonim, D.3
Golub, T.R.4
Kohane, I.S.5
-
9
-
-
0001622226
-
Toward a systematic determination of complex reaction mechanisms
-
Chevalier,T., Schreiber,I. and Ross,J. (1993) Toward a systematic determination of complex reaction mechanisms. J. Phys. Chem., 97, 6776-6787.
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 6776-6787
-
-
Chevalier, T.1
Schreiber, I.2
Ross, J.3
-
10
-
-
0038798081
-
Genomewide view of gene silencing by small interfering RNAs
-
Chi,J.T., Chang,H.Y., Wang,N.N., Chang,D.S., Dunphy,N. and Brown,P.O. (2003) Genomewide view of gene silencing by small interfering RNAs. Proc. Natl Acad. Sci. USA, 100, 6343-6346.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 6343-6346
-
-
Chi, J.T.1
Chang, H.Y.2
Wang, N.N.3
Chang, D.S.4
Dunphy, N.5
Brown, P.O.6
-
11
-
-
0032612220
-
Linear modeling of mRNA expression levels during CNS development and injury
-
D'Haeseleer,P., Wen,X., Fuhrman,S. and Somogyi,R. (1999) Linear modeling of mRNA expression levels during CNS development and injury. Pac. Symp. Biocomput., 41-52.
-
(1999)
Pac. Symp. Biocomput.
, pp. 41-52
-
-
D'Haeseleer, P.1
Wen, X.2
Fuhrman, S.3
Somogyi, R.4
-
12
-
-
0037686295
-
Killing the messenger: Short RNAs that silence gene expression
-
Dykxhoorn,D.M., Novina,C.D. and Sharp,P.A. (2003) Killing the messenger: short RNAs that silence gene expression. Nat. Rev. Mol. Cell. Biol., 4, 457-467.
-
(2003)
Nat. Rev. Mol. Cell. Biol.
, vol.4
, pp. 457-467
-
-
Dykxhoorn, D.M.1
Novina, C.D.2
Sharp, P.A.3
-
13
-
-
0033707946
-
Using Bayesian networks to analyze expression data
-
Friedman,N., Linial,M., Nachman,I. and Pe'er,D. (2000) Using Bayesian networks to analyze expression data. J. Comput. Biol., 7, 601-620.
-
(2000)
J. Comput. Biol.
, vol.7
, pp. 601-620
-
-
Friedman, N.1
Linial, M.2
Nachman, I.3
Pe'er, D.4
-
14
-
-
0038048325
-
Inferring genetic networks and identifying compound mode of action via expression profiling
-
Gardner,T.S., di Bernardo,D., Lorenz,D. and Collins,J.J. (2003) Inferring genetic networks and identifying compound mode of action via expression profiling. Science, 301, 102-105.
-
(2003)
Science
, vol.301
, pp. 102-105
-
-
Gardner, T.S.1
di Bernardo, D.2
Lorenz, D.3
Collins, J.J.4
-
15
-
-
0035221560
-
Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks
-
Hartemink,A.J., Gifford,D.K., Jaakkola,T.S. and Young,R.A. (2001) Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. Pac. Symp. Biocomput., 422-433.
-
(2001)
Pac. Symp. Biocomput.
, pp. 422-433
-
-
Hartemink, A.J.1
Gifford, D.K.2
Jaakkola, T.S.3
Young, R.A.4
-
16
-
-
0037685280
-
Expression profiling reveals off-target gene regulation by RNAi
-
Jackson,A.L., Bartz,S.R., Schelter,J., Kobayashi,S.V., Burchard,J., Mao,M., Li,B., Cavet,G. and Linsley,P.S. (2003) Expression profiling reveals off-target gene regulation by RNAi. Nat. Biotechnol. 21, 635-637.
-
(2003)
Nat. Biotechnol.
, vol.21
, pp. 635-637
-
-
Jackson, A.L.1
Bartz, S.R.2
Schelter, J.3
Kobayashi, S.V.4
Burchard, J.5
Mao, M.6
Li, B.7
Cavet, G.8
Linsley, P.S.9
-
17
-
-
0035799707
-
Lethality and centrality in protein networks
-
Jeong,H., Mason,S.P., Barabasi,A.L. and Oltvai,Z.N. (2001) Lethality and centrality in protein networks. Nature, 411, 41-42.
-
(2001)
Nature
, vol.411
, pp. 41-42
-
-
Jeong, H.1
Mason, S.P.2
Barabasi, A.L.3
Oltvai, Z.N.4
-
18
-
-
0034609791
-
The large-scale organization of metabolic networks
-
Jeong,H., Tombor,B., Albert,R., Oltvai,Z.N. and Barabasi,A.L. (2000) The large-scale organization of metabolic networks. Nature, 407, 651-654.
-
(2000)
Nature
, vol.407
, pp. 651-654
-
-
Jeong, H.1
Tombor, B.2
Albert, R.3
Oltvai, Z.N.4
Barabasi, A.L.5
-
19
-
-
0036789922
-
Untangling the wires: A strategy to trace functional interactions in signaling and gene networks
-
Kholodenko,B.N., Kiyatkin,A., Bruggeman,F.J., Sontag,E., Westerhoff,H.V. and Hoek,J.B. (2002) Untangling the wires: a strategy to trace functional interactions in signaling and gene networks. Proc. Natl Acad. Sci. USA, 99, 12841-12846.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 12841-12846
-
-
Kholodenko, B.N.1
Kiyatkin, A.2
Bruggeman, F.J.3
Sontag, E.4
Westerhoff, H.V.5
Hoek, J.B.6
-
20
-
-
0035230209
-
Reverse engineering of metabolic pathways from observed data using genetic programming
-
Koza,J.R., Mydlowec,W., Lanza,G., Yu,J. and Keane,M.A. (2001) Reverse engineering of metabolic pathways from observed data using genetic programming. Pac. Symp. Biocomput., 6, 434-445.
-
(2001)
Pac. Symp. Biocomput.
, vol.6
, pp. 434-445
-
-
Koza, J.R.1
Mydlowec, W.2
Lanza, G.3
Yu, J.4
Keane, M.A.5
-
21
-
-
0031616241
-
Reveal, a general reverse engineering algorithm for inference of genetic network architectures
-
Liang,S., Fuhrman,S. and Somogyi,R. (1998) Reveal, a general reverse engineering algorithm for inference of genetic network architectures. Pac. Symp. Biocomput., 18-29.
-
(1998)
Pac. Symp. Biocomput.
, pp. 18-29
-
-
Liang, S.1
Fuhrman, S.2
Somogyi, R.3
-
22
-
-
1842631431
-
Small interfering RNA production by enzymatic engineering of DNA (SPEED)
-
Luo,B., Heard,A.D. and Lodish,H.F. (2004) Small interfering RNA production by enzymatic engineering of DNA (SPEED). Proc. Natl Acad. Sci. USA, 101, 5494-5499.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 5494-5499
-
-
Luo, B.1
Heard, A.D.2
Lodish, H.F.3
-
23
-
-
0033083733
-
It's a noisy business! Genetic regulation at the nanomolar scale
-
McAdams,H.H. and Arkin,A. (1999) It's a noisy business! Genetic regulation at the nanomolar scale. Trends Genet., 15, 65-69.
-
(1999)
Trends Genet.
, vol.15
, pp. 65-69
-
-
McAdams, H.H.1
Arkin, A.2
-
24
-
-
0037174670
-
Network motifs: Simple building blocks of complex networks
-
Milo,R., Shen-Orr,S., Itzkovitz,S., Kashtan,N., Chklovskii,D. and Alon,U. (2002) Network motifs: simple building blocks of complex networks. Science, 298, 824-827.
-
(2002)
Science
, vol.298
, pp. 824-827
-
-
Milo, R.1
Shen-Orr, S.2
Itzkovitz, S.3
Kashtan, N.4
Chklovskii, D.5
Alon, U.6
-
25
-
-
12144288006
-
A resource for large-scale RNA-interference-based screens in mammals
-
Paddison,P.J., Silva,J.M., Conklin,D.S., Schlabach,M., Li,M., Aruleba,S., Balija,V., O'Shaughnessy,A., Gnoj,L., Scobie,K., Chang,K. et al. (2004) A resource for large-scale RNA-interference-based screens in mammals. Nature, 428, 427-431.
-
(2004)
Nature
, vol.428
, pp. 427-431
-
-
Paddison, P.J.1
Silva, J.M.2
Conklin, D.S.3
Schlabach, M.4
Li, M.5
Aruleba, S.6
Balija, V.7
O'Shaughnessy, A.8
Gnoj, L.9
Scobie, K.10
Chang, K.11
-
26
-
-
12344318183
-
Making the most of it: Pathway reconstruction and integrative simulation using the data at hand
-
Rice,J.J. and Stolovitzky,G.A. (2004) Making the most of it: pathway reconstruction and integrative simulation using the data at hand. Biosilico, 2, 70-77.
-
(2004)
Biosilico
, vol.2
, pp. 70-77
-
-
Rice, J.J.1
Stolovitzky, G.A.2
-
27
-
-
0036678794
-
Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics
-
Ronen,M., Rosenberg,R., Shraiman,B.I. and Alon,U. (2002) Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Proc. Natl Acad. Sci. USA, 99, 10555-10560.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 10555-10560
-
-
Ronen, M.1
Rosenberg, R.2
Shraiman, B.I.3
Alon, U.4
-
28
-
-
0036428761
-
Negative autoregulation speeds the response times of transcription networks
-
Rosenfeld,N., Elowitz,M.B. and Alon,U. (2002) Negative autoregulation speeds the response times of transcription networks. J. Mol. Biol., 323, 785-793.
-
(2002)
J. Mol. Biol.
, vol.323
, pp. 785-793
-
-
Rosenfeld, N.1
Elowitz, M.B.2
Alon, U.3
-
29
-
-
0041744850
-
On the deduction of chemical reaction pathways from measurements of time series of concentrations
-
Samoilov,M., Arkin,A. and Ross,J. (2001) On the deduction of chemical reaction pathways from measurements of time series of concentrations. Chaos, 11, 108-114.
-
(2001)
Chaos
, vol.11
, pp. 108-114
-
-
Samoilov, M.1
Arkin, A.2
Ross, J.3
-
30
-
-
0037941585
-
Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data
-
Segal,E., Shapira,M., Regev,A., Pe'er,D., Botstein,D., Koller,D. and Friedman,N. (2003) Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet., 34, 166-176.
-
(2003)
Nat. Genet.
, vol.34
, pp. 166-176
-
-
Segal, E.1
Shapira, M.2
Regev, A.3
Pe'er, D.4
Botstein, D.5
Koller, D.6
Friedman, N.7
-
31
-
-
0036578795
-
Network motifs in the transcriptional regulation network of Escherichia coli
-
Shen-Orr,S.S., Milo,R., Mangan,S. and Alon,U. (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet., 31, 64-68.
-
(2002)
Nat. Genet.
, vol.31
, pp. 64-68
-
-
Shen-Orr, S.S.1
Milo, R.2
Mangan, S.3
Alon, U.4
-
32
-
-
0041627865
-
Influence of network topology and data collection on network inference
-
Smith,V.A., Jarvis,E.D. and Hartemink,A.J. (2003) Influence of network topology and data collection on network inference. Pac. Symp. Biocomput., 164-175.
-
(2003)
Pac. Symp. Biocomput.
, pp. 164-175
-
-
Smith, V.A.1
Jarvis, E.D.2
Hartemink, A.J.3
-
33
-
-
0038492417
-
A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae)
-
Troyanskaya,O.G., Dolinski,K., Owen,A.B., Altman,R.B. and Botstein,D. (2003) A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc. Natl Acad. Sci., USA, 100, 8348-8353.
-
(2003)
Proc. Natl. Acad. Sci., USA
, vol.100
, pp. 8348-8353
-
-
Troyanskaya, O.G.1
Dolinski, K.2
Owen, A.B.3
Altman, R.B.4
Botstein, D.5
-
34
-
-
0034628508
-
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
-
Uetz,P., Giot,L., Cagney,G., Mansfield,T.A., Judson,R.S., Knight,J.R., Lockshon,D., Narayan,V., Srinivasan,M., Pochart,P., Qureshi-Emili,A. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-627.
-
(2000)
Nature
, vol.403
, 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
-
35
-
-
0036020655
-
Genetic network modeling
-
van Someren,E.P., Wessels,L.F., Backer,E. and Reinders,M.J. (2002) Genetic network modeling. Pharmacogenomics, 3, 507-525.
-
(2002)
Pharmacogenomics
, vol.3
, pp. 507-525
-
-
van Someren, E.P.1
Wessels, L.F.2
Backer, E.3
Reinders, M.J.4
-
36
-
-
0036177681
-
Estimating coarse gene network structure from large-scale gene perturbation data
-
Wagner,A. (2002) Estimating coarse gene network structure from large-scale gene perturbation data. Genome Res., 12, 309-315.
-
(2002)
Genome Res.
, vol.12
, pp. 309-315
-
-
Wagner, A.1
-
37
-
-
0034729586
-
A fuzzy logic approach to analyzing gene expression data
-
Woolf,P.J. and Wang,Y. (2000) A fuzzy logic approach to analyzing gene expression data. Physiol. Genomics, 3, 9-15.
-
(2000)
Physiol. Genomics
, vol.3
, pp. 9-15
-
-
Woolf, P.J.1
Wang, Y.2
-
38
-
-
0037197936
-
Reverse engineering gene networks using singular value decomposition and robust regression
-
Yeung,M.K., Tegner,J. and Collins,J.J. (2002) Reverse engineering gene networks using singular value decomposition and robust regression. Proc. Natl Acad. Sci. USA, 99, 6163-6168.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 6163-6168
-
-
Yeung, M.K.1
Tegner, J.2
Collins, J.J.3
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