-
1
-
-
77955481403
-
Stochastic Oscillations in Genetic Regulatory Networks. Applications to Microarray Experiment, COMPSTAT- 2006
-
in: Rizzi A, Vichi M Edtiors
-
Rosenfeld S. Stochastic Oscillations in Genetic Regulatory Networks. Applications to Microarray Experiment, in: Rizzi A, Vichi M Edtiors. COMPSTAT- 2006. Physica-Verlag. 2006; p. 1609-18.
-
(2006)
Physica-Verlag
, pp. 1609-1618
-
-
Rosenfeld, S.1
-
2
-
-
79958791734
-
-
in: Gauges R, Kummer U, Pahle J, Willy P, Edtiors, University of Heidelberg, Heidelberg
-
Rosenfeld S. Why do high-dimensional networks seem to be stable?-A reflection on stochasticity of dynamically unstable nonlinear systems, in: Gauges R, Kummer U, Pahle J, Willy P, Edtiors. Fifth Workshop on Computation of Biochemical Pathways and Genetic Networks, University of Heidelberg, Heidelberg, 2008, p. 101-12.
-
(2008)
Why Do High-dimensional Networks Seem to Be Stable?-A Reflection On Stochasticity of Dynamically Unstable Nonlinear Systems, Fifth Workshop On Computation of Biochemical Pathways and Genetic Networks
, pp. 101-112
-
-
Rosenfeld, S.1
-
4
-
-
84944263050
-
Making the most of microarrays
-
Editorial
-
Editorial, Making the most of microarrays. Nature Biotechnology. 2006; 24:1039.
-
(2006)
Nature Biotechnology
, vol.24
, pp. 1039
-
-
-
5
-
-
33748491517
-
The MicroArray Quality Control (MAQC) project shows interand intraplatform reproducibility of gene expression measurements
-
Shi L, et al. The MicroArray Quality Control (MAQC) project shows interand intraplatform reproducibility of gene expression measurements. Nature Biotechnology. 2006;24:1151.
-
(2006)
Nature Biotechnology
, vol.24
, pp. 1151
-
-
Shi, L.1
-
6
-
-
8444246272
-
QA/QC: Challenges and pitfalls facing the microarray community and regulatory agencies
-
Shi L, et al. QA/QC: challenges and pitfalls facing the microarray community and regulatory agencies. Expert Rev Mol Diagn. 2004;4:761.
-
(2004)
Expert Rev Mol Diagn
, vol.4
, pp. 761
-
-
Shi, L.1
-
7
-
-
13444304216
-
Microarrays and molecular research: Noise discovery?
-
Ioannidis JP. Microarrays and molecular research: noise discovery? Lancet. 2005;365:454.
-
(2005)
Lancet
, vol.365
, pp. 454
-
-
Ioannidis, J.P.1
-
8
-
-
13844308671
-
Gene-expression profiling in breast cancer
-
Jenssen TK, Hovig E. Gene-expression profiling in breast cancer. Lancet. 2005;365:634.
-
(2005)
Lancet
, vol.365
, pp. 634
-
-
Jenssen, T.K.1
Hovig, E.2
-
10
-
-
0038697629
-
The interplay of nuclear mRNP assembly, mRNA surveillance and export
-
Stutz F, Izaurralde E. The interplay of nuclear mRNP assembly, mRNA surveillance and export. Trends Cell Biol. 2003;13:319.
-
(2003)
Trends Cell Biol
, vol.13
, pp. 319
-
-
Stutz, F.1
Izaurralde, E.2
-
11
-
-
77955483551
-
Characteristics of transcriptional activity in nonlinear dynamics of genetic regulatory networks
-
Rosenfeld S. Characteristics of transcriptional activity in nonlinear dynamics of genetic regulatory networks. Gene Regul Syst Bio. 2009; 3:159.
-
(2009)
Gene Regul Syst Bio
, vol.3
, pp. 159
-
-
Rosenfeld, S.1
-
13
-
-
25144492110
-
Approximative kinetic formats used in metabolic network modeling
-
Heijnen JJ. Approximative kinetic formats used in metabolic network modeling. Biotechnol Bioeng. 2005;91:534.
-
(2005)
Biotechnol Bioeng
, vol.91
, pp. 534
-
-
Heijnen, J.J.1
-
14
-
-
84876731888
-
Computational Models of Metabolism: Stability and Regulation in Metabolic Networks
-
in press
-
Steuer R, Junker B. Computational Models of Metabolism: Stability and Regulation in Metabolic Networks, Advances of Chemical Physics (in press) (2009).
-
(2009)
Advances of Chemical Physics
-
-
Steuer, R.1
Junker, B.2
-
15
-
-
65249141709
-
Database for mRNA half-life of 19,977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells
-
Sharova LV, et al. Database for mRNA half-life of 19,977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells. DNA Res. 2009;16:45.
-
(2009)
DNA Res
, vol.16
, pp. 45
-
-
Sharova, L.V.1
-
16
-
-
0037197892
-
Precision and functional specificity in mRNA decay
-
Wang Y, et al. Precision and functional specificity in mRNA decay. Proc Natl Acad Sci U S A. 2002;99:5860.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 5860
-
-
Wang, Y.1
-
17
-
-
0042330135
-
Genome-wide survey of mRNA halflives in Bacillus subtilis identifies extremely stable mRNAs
-
Hambraeus G, von WC, Hederstedt L. Genome-wide survey of mRNA halflives in Bacillus subtilis identifies extremely stable mRNAs. Mol Genet Genomics. 2003;269:706.
-
(2003)
Mol Genet Genomics
, vol.269
, pp. 706
-
-
Hambraeus, G.1
Von, W.C.2
Hederstedt, L.3
-
18
-
-
0037115826
-
Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes
-
Raghavan A, et al. Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes. Nucleic Acids Res. 2002;30:5529.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 5529
-
-
Raghavan, A.1
-
19
-
-
4644288309
-
Microarray-based analyses of mRNA decay in the regulation of mammalian gene expression
-
Raghavan A, Bohjanen PR. Microarray-based analyses of mRNA decay in the regulation of mammalian gene expression. Brief Funct Genomic Proteomic. 2004;3:112.
-
(2004)
Brief Funct Genomic Proteomic
, vol.3
, pp. 112
-
-
Raghavan, A.1
Bohjanen, P.R.2
-
20
-
-
0025952599
-
A comparison of apparent mRNA half-life using kinetic labeling techniques vs. decay following administration of transcriptional inhibitors
-
Harrold S, Genovese C, Kobrin B, Morrison SL, Milcarek C. A comparison of apparent mRNA half-life using kinetic labeling techniques vs. decay following administration of transcriptional inhibitors. Anal Biochem. 1991;198:19.
-
(1991)
Anal Biochem
, vol.198
, pp. 19
-
-
Harrold, S.1
Genovese, C.2
Kobrin, B.3
Morrison, S.L.4
Milcarek, C.5
-
21
-
-
3242726930
-
Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms
-
Garcia-Martinez J, Aranda A, Perez-Ortin JE. Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms. Mol Cell. 2004;15:303.
-
(2004)
Mol Cell
, vol.15
, pp. 303
-
-
Garcia-Martinez, J.1
Aranda, A.2
Perez-Ortin, J.E.3
-
23
-
-
35348898041
-
Stochastic cooperativity in non-linear dynamics of genetic regulatory networks
-
Rosenfeld S. Stochastic cooperativity in non-linear dynamics of genetic regulatory networks. Math Biosci. 2007;210:121.
-
(2007)
Math Biosci
, vol.210
, pp. 121
-
-
Rosenfeld, S.1
-
25
-
-
0027499733
-
Soluble proteins: Size, shape and function
-
Goodsell DS, Olson AJ. Soluble proteins: size, shape and function. Trends Biochem Sci. 1993;18:65.
-
(1993)
Trends Biochem Sci
, vol.18
, pp. 65
-
-
Goodsell, D.S.1
Olson, A.J.2
-
26
-
-
0033779678
-
Diffusional protein transport within the nucleus: A message in the medium
-
Pederson T. Diffusional protein transport within the nucleus: a message in the medium. Nat Cell Biol. 2000;2:E73.
-
(2000)
Nat Cell Biol
, vol.2
-
-
Pederson, T.1
-
27
-
-
33746649820
-
Single molecule measurements of repressor protein 1D diffusion on DNA
-
Wang YM, Austin RH, Cox EC. Single molecule measurements of repressor protein 1D diffusion on DNA. Phys Rev Lett. 2006;97:048302.
-
(2006)
Phys Rev Lett
, vol.97
, pp. 048302
-
-
Wang, Y.M.1
Austin, R.H.2
Cox, E.C.3
-
28
-
-
0036204260
-
Protein-water interactions
-
Parsegian VA. Protein-water interactions. Int Rev Cytol. 2002;215:1.
-
(2002)
Int Rev Cytol
, vol.215
, pp. 1
-
-
Parsegian, V.A.1
-
29
-
-
0035478585
-
Macromolecular crowding: Obvious but underappreciated
-
Ellis RJ. Macromolecular crowding: obvious but underappreciated. Trends Biochem Sci. 2001;26:597.
-
(2001)
Trends Biochem Sci
, vol.26
, pp. 597
-
-
Ellis, R.J.1
-
30
-
-
35348918883
-
Stochastic Simulation of Chemical Kinetics
-
Gillespie DT. Stochastic Simulation of Chemical Kinetics. Annu Rev Phys Chem. 2006.
-
(2006)
Annu Rev Phys Chem
-
-
Gillespie, D.T.1
-
31
-
-
0842265974
-
Regulation of RNA polymerase II transcription by sequencespecific DNA binding factors
-
Kadonaga JT. Regulation of RNA polymerase II transcription by sequencespecific DNA binding factors. Cell. 2004;116:247.
-
(2004)
Cell
, vol.116
, pp. 247
-
-
Kadonaga, J.T.1
-
32
-
-
77953409526
-
Patterns of stochastic behavior in dynamically unstable highdimensional biochemical networks
-
Rosenfeld S. Patterns of stochastic behavior in dynamically unstable highdimensional biochemical networks. Gene Regul Syst Bio. 2009;3:1.
-
(2009)
Gene Regul Syst Bio
, vol.3
, pp. 1
-
-
Rosenfeld, S.1
-
33
-
-
33645027986
-
Stochastic protein expression in individual cells at the single molecule level
-
Cai L, Friedman N, Xie XS. Stochastic protein expression in individual cells at the single molecule level. Nature. 2006;440:358.
-
(2006)
Nature
, vol.440
, pp. 358
-
-
Cai, L.1
Friedman, N.2
Xie, X.S.3
-
34
-
-
15544371346
-
Gene regulation at the single-cell level
-
Rosenfeld N, Young JW, Alon U, Swain PS, Elowitz MB. Gene regulation at the single-cell level. Science. 2005;307:1962.
-
(2005)
Science
, vol.307
, pp. 1962
-
-
Rosenfeld, N.1
Young, J.W.2
Alon, U.3
Swain, P.S.4
Elowitz, M.B.5
-
35
-
-
0032167516
-
Transcription occurs in pulses in muscle fibers
-
Newlands S, et al. Transcription occurs in pulses in muscle fibers. Genes Dev. 1998;12:2748.
-
(1998)
Genes Dev
, vol.12
, pp. 2748
-
-
Newlands, S.1
-
36
-
-
0028328719
-
Transcription of individual genes in eukaryotic cells occurs randomly and infrequently
-
Ross IL, Browne CM, Hume DA. Transcription of individual genes in eukaryotic cells occurs randomly and infrequently, Immunol. Cell Biol. 1994;72:177.
-
(1994)
Immunol. Cell Biol
, vol.72
, pp. 177
-
-
Ross, I.L.1
Browne, C.M.2
Hume, D.A.3
-
38
-
-
3843126332
-
RNA dynamics in live Escherichia coli cells
-
Golding I, Cox EC. RNA dynamics in live Escherichia coli cells. Proc Natl Acad Sci U S A. 2004;101:11310.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 11310
-
-
Golding, I.1
Cox, E.C.2
-
39
-
-
28944434119
-
Real-time kinetics of gene activity in individual bacteria
-
Golding I, Paulsson J, Zawilski SM, Cox EC. Real-time kinetics of gene activity in individual bacteria. Cell. 2005;123:1025.
-
(2005)
Cell
, vol.123
, pp. 1025
-
-
Golding, I.1
Paulsson, J.2
Zawilski, S.M.3
Cox, E.C.4
-
40
-
-
33645033645
-
Probing gene expression in live cells, one protein molecule at a time
-
Yu J, Xiao J, Ren X, Lao K, Xie XS. Probing gene expression in live cells, one protein molecule at a time. Science. 2006;311:1600.
-
(2006)
Science
, vol.311
, pp. 1600
-
-
Yu, J.1
Xiao, J.2
Ren, X.3
Lao, K.4
Xie, X.S.5
-
42
-
-
0033083733
-
It's a noisy business! Genetic regulation at the nanomolar scale
-
McAdams HH, Arkin A. It's a noisy business! Genetic regulation at the nanomolar scale. Trends Genet. 1999;15:65.
-
(1999)
Trends Genet
, vol.15
, pp. 65
-
-
McAdams, H.H.1
Arkin, A.2
-
44
-
-
0035193294
-
Stochasticity in Transcriptional Regulation: Origins, Consequences, and Mathematical Representations
-
Kepler T, Eiston T. Stochasticity in Transcriptional Regulation: Origins, Consequences, and Mathematical Representations. Biophysical Journal. 2001;81:3116.
-
(2001)
Biophysical Journal
, vol.81
, pp. 3116
-
-
Kepler, T.1
Eiston, T.2
-
45
-
-
0036729047
-
Can a biologist fix a radio?-Or, what I learned while studying apoptosis
-
Lazebnik Y. Can a biologist fix a radio?-Or, what I learned while studying apoptosis. Cancer Cell. 2002;2:179.
-
(2002)
Cancer Cell
, vol.2
, pp. 179
-
-
Lazebnik, Y.1
-
48
-
-
77955487010
-
Mathematical Description of Biochemical Networks: Instability, stochasticity, evolution
-
in: Thiangliam S Edtior, Oxford University Press
-
Rosenfeld S. Mathematical Description of Biochemical Networks: instability, stochasticity, evolution, in: Thiangliam S Edtior. Systems Biology of Cancer, Oxford University Press, 2009.
-
(2009)
Systems Biology of Cancer
-
-
Rosenfeld, S.1
-
49
-
-
0015514970
-
Will a large complex system be stable?
-
May RM. Will a large complex system be stable? Nature. 1972;238:413.
-
(1972)
Nature
, vol.238
, pp. 413
-
-
May, R.M.1
-
50
-
-
60349119161
-
Reaction systems, graph theory and dynamical networks
-
in: Gauges R, Kummer U, Pahle J, Willy P Editors, University of Heidelberg, Heidelberg
-
Kirkilionis M. Reaction systems, graph theory and dynamical networks, in: Gauges R, Kummer U, Pahle J, Willy P Editors. Fifth Workshop on Computation of Biochemical Pathways and Genetic Networks, University of Heidelberg, Heidelberg, 2008.
-
(2008)
Fifth Workshop On Computation of Biochemical Pathways and Genetic Networks
-
-
Kirkilionis, M.1
-
51
-
-
33745711647
-
Estimations of intrinsic and extrinsic noise in models of nonlinear genetic networks
-
Scott M, Ingalls B, Kaern M. Estimations of intrinsic and extrinsic noise in models of nonlinear genetic networks. Chaos. 2006;16:026107.
-
(2006)
Chaos
, vol.16
, pp. 026107
-
-
Scott, M.1
Ingalls, B.2
Kaern, M.3
-
53
-
-
0041530047
-
Resampling-based Multiple Testing for Microarray Data Analysis
-
Ge Y, Dudoit S, Speed T. Resampling-based Multiple Testing for Microarray Data Analysis. Test. 2003;12:1.
-
(2003)
Test
, vol.12
, pp. 1
-
-
Ge, Y.1
Dudoit, S.2
Speed, T.3
-
54
-
-
77955503279
-
Detection of Differentially Expressed Genes In Small Sets of cDNA Microarrays
-
Rosenfeld S. Detection of Differentially Expressed Genes In Small Sets of cDNA Microarrays. Journal of Data Science. 2007;5:451.
-
(2007)
Journal of Data Science
, vol.5
, pp. 451
-
-
Rosenfeld, S.1
-
55
-
-
74549174585
-
DNA microarrays are predictive of cancer prognosis: A reevaluation
-
Fan X, et al. DNA microarrays are predictive of cancer prognosis: a reevaluation. Clin Cancer Res. 2010;16:629.
-
(2010)
Clin Cancer Res
, vol.16
, pp. 629
-
-
Fan, X.1
-
56
-
-
33751193656
-
Converting a breast cancer microarray signature into a highthroughput diagnostic test
-
Glas AM, et al. Converting a breast cancer microarray signature into a highthroughput diagnostic test. BMC Genomics. 2006;7:278.
-
(2006)
BMC Genomics
, vol.7
, pp. 278
-
-
Glas, A.M.1
-
57
-
-
34147164024
-
Is molecular profiling ready for use in clinical decision making?
-
Ioannidis JP. Is molecular profiling ready for use in clinical decision making? Oncologist. 2007;12:301.
-
(2007)
Oncologist
, vol.12
, pp. 301
-
-
Ioannidis, J.P.1
-
58
-
-
58749109439
-
Personalized genetic prediction: Too limited, too expensive, or too soon?
-
Ioannidis JP. Personalized genetic prediction: too limited, too expensive, or too soon? Ann Intern Med. 2009;150:139.
-
(2009)
Ann Intern Med
, vol.150
, pp. 139
-
-
Ioannidis, J.P.1
|