-
1
-
-
84940644968
-
A mathematical theory of communication
-
Shannon C. 1948 A mathematical theory of communication. Bell Syst. Tech. J. 27, 379-423. (doi:10.1002/j.1538-7305.1948.tb01338.x).
-
(1948)
Bell Syst. Tech. J.
, vol.27
, pp. 379-423
-
-
Shannon, C.1
-
2
-
-
24344458137
-
Feature selection based on mutual information: Criteria of max-dependency, max-relevance, and minredundancy
-
Peng H, Long F, Ding C. 2005 Feature selection based on mutual information: criteria of max-dependency, max-relevance, and minredundancy. IEEE Trans. Pattern Anal. Mach. Intell. 27, 1226-1238. (doi:10.1109/TPAMI.2005.159).
-
(2005)
IEEE Trans. Pattern Anal. Mach. Intell.
, vol.27
, pp. 1226-1238
-
-
Peng, H.1
Long, F.2
Ding, C.3
-
4
-
-
80054841161
-
Information transduction capacity of noisy biochemical signaling networks
-
Cheong R, Rhee A, Wang CJ, Nemenman I, Levchenko A. 2011 Information transduction capacity of noisy biochemical signaling networks. Science 334, 354-358. (doi:10.1126/science.1204553).
-
(2011)
Science
, vol.334
, pp. 354-358
-
-
Cheong, R.1
Rhee, A.2
Wang, C.J.3
Nemenman, I.4
Levchenko, A.5
-
5
-
-
84881033077
-
Robustness and compensation of information transmission of signaling pathways
-
Uda S, Saito TH, Kudo T, Kokaji T, Tsuchiya T, Kubota H, Komori Y, Ozaki Y-I, Kuroda S. 2013 Robustness and compensation of information transmission of signaling pathways. Science 341, 558-561. (doi:10.1126/science.1234511).
-
(2013)
Science
, vol.341
, pp. 558-561
-
-
Uda, S.1
Saito, T.H.2
Kudo, T.3
Kokaji, T.4
Tsuchiya, T.5
Kubota, H.6
Komori, Y.7
Ozaki, Y.-I.8
Kuroda, S.9
-
6
-
-
70349866271
-
Maximum likelihood and the single receptor
-
Endres RG, Wingreen NS. 2009 Maximum likelihood and the single receptor. Phys. Rev. Lett. 103, 158101. (doi:10.1103/PhysRevLett.103.158101).
-
(2009)
Phys. Rev. Lett.
, vol.103
, pp. 158101
-
-
Endres, R.G.1
Wingreen, N.S.2
-
7
-
-
34548378653
-
An informationtheoretic characterization of the optimal gradient sensing response of cells
-
Andrews BW, Iglesias PA. 2007 An informationtheoretic characterization of the optimal gradient sensing response of cells. PLoS Comput. Biol. 3, e153. (doi:10.1371/journal.pcbi.0030153).
-
(2007)
PLoS Comput. Biol
, vol.3
, pp. e153
-
-
Andrews, B.W.1
Iglesias, P.A.2
-
8
-
-
79953652546
-
Information transmission in genetic regulatory networks: A review
-
Tkačik G, Walczak AM. 2011 Information transmission in genetic regulatory networks: A review. J. Phys. Condensed Matter 23, 153102. (doi:10.1088/0953-8984/23/15/153102).
-
(2011)
J. Phys. Condensed Matter
, vol.23
, pp. 153102
-
-
Tkačik, G.1
Walczak, A.M.2
-
9
-
-
84858115857
-
Reliability of frequency and amplitude decoding in gene regulation
-
Tostevin F, de-Ronde W, ten-Wolde PR. 2012 Reliability of frequency and amplitude decoding in gene regulation. Phys. Rev. Lett. 108, 108104. (doi:10.1103/PhysRevLett.108.108104).
-
(2012)
Phys. Rev. Lett
, vol.108
, pp. 108104
-
-
Tostevin, F.1
De-Ronde, W.2
Ten-Wolde, P.R.3
-
10
-
-
84864959012
-
The application of information theory to biochemical signaling systems
-
Rhee A, Cheong R, Levchenko A. 2012 The application of information theory to biochemical signaling systems. Phys. Biol. 9, 045011. (doi:10.1088/1478-3975/9/4/045011).
-
(2012)
Phys. Biol.
, vol.9
, pp. 045011
-
-
Rhee, A.1
Cheong, R.2
Levchenko, A.3
-
11
-
-
84908897496
-
Information theory and signal transduction systems: From molecular information processing to network inference
-
McMahon SS, Sim A, Filippi S, Johnson R, Liepe J, Smith D, Stumpf MP. 2014 Information theory and signal transduction systems: from molecular information processing to network inference. Semin. Cell Dev. Biol. 35, 98-108. (doi:10.1016/j.semcdb.2014.06.011).
-
(2014)
Semin. Cell Dev. Biol.
, vol.35
, pp. 98-108
-
-
McMahon, S.S.1
Sim, A.2
Filippi, S.3
Johnson, R.4
Liepe, J.5
Smith, D.6
Stumpf, M.P.7
-
12
-
-
50449096238
-
Information flow and optimization in transcriptional regulation
-
Tkacik G, Callan CG, Bialek W. 2008 Information flow and optimization in transcriptional regulation. Proc. Natl Acad. Sci. USA 105, 12265-12270. (doi:10.1073/pnas.0806077105).
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 12265-12270
-
-
Tkacik, G.1
Callan, C.G.2
Bialek, W.3
-
13
-
-
66349109628
-
Mutual information between input and output trajectories of biochemical networks
-
Tostevin F, ten-Wolde PR. 2009 Mutual information between input and output trajectories of biochemical networks. Phys. Rev. Lett. 102, 218101. (doi:10.1103/PhysRevLett.102.218101).
-
(2009)
Phys. Rev. Lett.
, vol.102
, pp. 218101
-
-
Tostevin, F.1
Ten-Wolde, P.R.2
-
14
-
-
84859526141
-
Optimizing information flow in small genetic networks. III. A self-interacting gene
-
Tkacik G, Walczak AM, Bialek W. 2012 Optimizing information flow in small genetic networks. III. A self-interacting gene. Phys. Rev. E 85, 041903. (doi:10.1103/PhysRevE.85.041903).
-
(2012)
Phys. Rev. E
, vol.85
, pp. 041903
-
-
Tkacik, G.1
Walczak, A.M.2
Bialek, W.3
-
15
-
-
84863580661
-
A framework for designing and analyzing binary decision-making strategies in cellular systems
-
Porter JR, Andrews BW, Iglesias PA. 2012 A framework for designing and analyzing binary decision-making strategies in cellular systems. Integr. Biol. 4, 310-317. (doi:10.1039/c2ib00114d).
-
(2012)
Integr. Biol.
, vol.4
, pp. 310-317
-
-
Porter, J.R.1
Andrews, B.W.2
Iglesias, P.A.3
-
16
-
-
84918571678
-
Accurate information transmission through dynamic biochemical signaling networks
-
Selimkhanov J, Taylor B, Yao J, Pilko A, Albeck J, Hoffmann A, Tsimring L, Wollman R. 2014 Accurate information transmission through dynamic biochemical signaling networks. Science 346, 1370-1373. (doi:10.1126/science.1254933).
-
(2014)
Science
, vol.346
, pp. 1370-1373
-
-
Selimkhanov, J.1
Taylor, B.2
Yao, J.3
Pilko, A.4
Albeck, J.5
Hoffmann, A.6
Tsimring, L.7
Wollman, R.8
-
17
-
-
48349119924
-
Information capacity of genetic regulatory elements
-
Tkacik G, Callan CG, Bialek W. 2008 Information capacity of genetic regulatory elements. Phys. Rev. E 78, 011910. (doi:10.1103/PhysRevE.78.011910).
-
(2008)
Phys. Rev. E
, vol.78
, pp. 011910
-
-
Tkacik, G.1
Callan, C.G.2
Bialek, W.3
-
18
-
-
80053153518
-
Architecture, constraints, and behavior
-
Doyle JC, Csete M. 2011 Architecture, constraints, and behavior. Proc. Natl Acad. Sci. USA 108(Suppl 3), 15624-15630. (doi:10.1073/pnas.1103557108).
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 15624-15630
-
-
Doyle, J.C.1
Csete, M.2
-
19
-
-
0037376655
-
Sniffers, buzzers, toggles and blinkers: Dynamics of regulatory and signaling pathways in the cell
-
Tyson JJ, Chen KC, Novák B. 2003 Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr. Opin. Cell Biol. 15, 221-231. (doi:10.1016/S0955-0674(03)00017-6).
-
(2003)
Curr. Opin. Cell Biol.
, vol.15
, pp. 221-231
-
-
Tyson, J.J.1
Chen, K.C.2
Novák, B.3
-
20
-
-
49549092691
-
Protein-protein interactions: From global to local analyses
-
Kelly WP, Stumpf MPH. 2008 Protein-protein interactions: from global to local analyses. Curr. Opin. Biotechnol. 19, 396-403. (doi:10.1016/j.copbio.2008.06.010).
-
(2008)
Curr. Opin. Biotechnol.
, vol.19
, pp. 396-403
-
-
Kelly, W.P.1
Stumpf, M.P.H.2
-
21
-
-
84900990155
-
Environmental sensing, information transfer, and cellular decision-making
-
Bowsher CG, Swain PS. 2014 Environmental sensing, information transfer, and cellular decision-making. Curr. Opin. Biotechnol. 28C, 149-155. (doi:10.1016/j.copbio.2014.04.010).
-
(2014)
Curr. Opin. Biotechnol
, vol.28 C
, pp. 149-155
-
-
Bowsher, C.G.1
Swain, P.S.2
-
22
-
-
84861204172
-
Identifying sources of variation and the flow of information in biochemical networks
-
Bowsher CG, Swain PS. 2012 Identifying sources of variation and the flow of information in biochemical networks. Proc. Natl Acad. Sci. USA 109, E1320-E1328. (doi:10.1073/pnas.1119407109).
-
(2012)
Proc. Natl Acad. Sci. USA
, vol.109
, pp. E1320-E1328
-
-
Bowsher, C.G.1
Swain, P.S.2
-
23
-
-
84876357659
-
Decomposing noise in biochemical signaling systems highlights the role of protein degradation
-
Komorowski M, Miekisz J, Stumpf MPH. 2013 Decomposing noise in biochemical signaling systems highlights the role of protein degradation. Biophys. J. 104, 1783-1793. (doi:10.1016/j.bpj.2013.02.027).
-
(2013)
Biophys. J.
, vol.104
, pp. 1783-1793
-
-
Komorowski, M.1
Miekisz, J.2
Stumpf, M.P.H.3
-
24
-
-
84875976767
-
The fidelity of dynamic signaling by noisy biomolecular networks
-
Bowsher CG, Voliotis M, Swain PS. 2013 The fidelity of dynamic signaling by noisy biomolecular networks. PLoS Comput. Biol. 9, e1002965. (doi:10.1371/journal.pcbi.1002965).
-
(2013)
PLoS Comput. Biol
, vol.9
, pp. e1002965
-
-
Bowsher, C.G.1
Voliotis, M.2
Swain, P.S.3
-
25
-
-
0036790975
-
Intrinsic and extrinsic contributions to stochasticity in gene expression
-
Swain PS, Elowitz MB, Siggia ED. 2002 Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc. Natl Acad. Sci. USA 99, 12795- 12800. (doi:10.1073/pnas.162041399).
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 12795-12800
-
-
Swain, P.S.1
Elowitz, M.B.2
Siggia, E.D.3
-
26
-
-
84875984016
-
Combined model of intrinsic and extrinsic variability for computational network design with application to synthetic biology
-
Toni T, Tidor B. 2013 Combined model of intrinsic and extrinsic variability for computational network design with application to synthetic biology. PLoS Comput. Biol. 9, e1002960. (doi:10.1371/journal.pcbi.1002960).
-
(2013)
PLoS Comput. Biol.
, vol.9
, pp. e1002960
-
-
Toni, T.1
Tidor, B.2
-
27
-
-
27944469202
-
Statistical validation of mutual information calculations: Comparison of alternative numerical algorithms
-
Cellucci CJ, Albano AM, Rapp PE. 2005 Statistical validation of mutual information calculations: comparison of alternative numerical algorithms. Phys. Rev. E 71, 066208. (doi:10.1103/PhysRevE.71.066208).
-
(2005)
Phys. Rev. E
, vol.71
, pp. 066208
-
-
Cellucci, C.J.1
Albano, A.M.2
Rapp, P.E.3
-
28
-
-
77952862003
-
Mutual information is critically dependent on prior assumptions: Would the correct estimate of mutual information please identify itself?
-
Oxford, England
-
Fernandes AD, Gloor GB. 2010 Mutual information is critically dependent on prior assumptions: would the correct estimate of mutual information please identify itself? Bioinformatics (Oxford, England) 26, 1135-1139. (doi:10.1093/bioinformatics/btq111).
-
(2010)
Bioinformatics
, vol.26
, pp. 1135-1139
-
-
Fernandes, A.D.1
Gloor, G.B.2
-
29
-
-
42549099171
-
Optimal signal processing in small stochastic biochemical networks
-
Ziv E, Nemenman I, Wiggins CH. 2007 Optimal signal processing in small stochastic biochemical networks. PLoS ONE 2, e1077. (doi:10.1371/journal.pone.0001077).
-
(2007)
PLoS ONE
, vol.2
, pp. e1077
-
-
Ziv, E.1
Nemenman, I.2
Wiggins, C.H.3
-
30
-
-
84930733410
-
A mutual information estimator with exponentially decaying bias
-
Zhang Z, Zheng L. 2015 A mutual information estimator with exponentially decaying bias. Stat. Appl. Genet. Mol. 14, 243-252. (doi:10.1515/sagmb-2014-0047).
-
(2015)
Stat. Appl. Genet. Mol.
, vol.14
, pp. 243-252
-
-
Zhang, Z.1
Zheng, L.2
-
31
-
-
0042526388
-
The mutual information: Detecting and evaluating dependencies between variables
-
Steuer R, Kurths J, Daub CO, Weise J, Selbig J. 2002 The mutual information: detecting and evaluating dependencies between variables. Bioinformatics 18(Suppl. 2), S231-S240. (doi:10.1093/bioinformatics/18.suppl-2.S231).
-
(2002)
Bioinformatics
, vol.18
, pp. S231-S240
-
-
Steuer, R.1
Kurths, J.2
Daub, C.O.3
Weise, J.4
Selbig, J.5
-
33
-
-
0004156740
-
-
New York, NY: Springer Science & Business Media
-
Nelsen RB. 2007 An introduction to copulas. New York, NY: Springer Science & Business Media.
-
(2007)
An Introduction to Copulas
-
-
Nelsen, R.B.1
-
34
-
-
84867122511
-
Linear noise approximation is valid over limited times for any chemical system that is sufficiently large
-
Wallace EWJ, Gillespie DT, Sanft KR, Petzold LR. 2012 Linear noise approximation is valid over limited times for any chemical system that is sufficiently large. IET Syst. Biol. 6, 102-115. (doi:10.1049/iet-syb.2011.0038).
-
(2012)
IET Syst. Biol
, vol.6
, pp. 102-115
-
-
Wallace, E.W.J.1
Gillespie, D.T.2
Sanft, K.R.3
Petzold, L.R.4
-
35
-
-
71749100925
-
Bayesian inference of biochemical kinetic parameters using the linear noise approximation
-
Komorowski M, Finkenstädt B, Harper CV, Rand DA. 2009 Bayesian inference of biochemical kinetic parameters using the linear noise approximation. BMC Bioinformatics 10, 343. (doi:10.1186/1471-2105-10-343).
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 343
-
-
Komorowski, M.1
Finkenstädt, B.2
Harper, C.V.3
Rand, D.A.4
-
36
-
-
78650556702
-
Stochastic reaction-diffusion kinetics in the microscopic limit
-
Fange D, Berg OG, Sjöberg P, Elf J. 2010 Stochastic reaction-diffusion kinetics in the microscopic limit. Proc. Natl Acad. Sci. USA 107, 19820-19825. (doi:10.1073/pnas.1006565107).
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 19820-19825
-
-
Fange, D.1
Berg, O.G.2
Sjöberg, P.3
Elf, J.4
-
37
-
-
79957743805
-
Sensitivity, robustness, and identifiability in stochastic chemical kinetics models
-
Komorowski M, Costa MJ, Rand DA, Stumpf MPH. 2011 Sensitivity, robustness, and identifiability in stochastic chemical kinetics models. Proc. Natl Acad. Sci. USA 108, 8645-8650. (doi:10.1073/pnas.1015814108).
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 8645-8650
-
-
Komorowski, M.1
Costa, M.J.2
Rand, D.A.3
Stumpf, M.P.H.4
-
38
-
-
84857816317
-
StochSens-Matlab package for sensitivity analysis of stochastic chemical systems
-
Komorowski M, Zurauskiene J, Stumpf MPH. 2012 StochSens-Matlab package for sensitivity analysis of stochastic chemical systems. Bioinformatics 28, 731-733. (doi:10.1093/bioinformatics/btr714).
-
(2012)
Bioinformatics
, vol.28
, pp. 731-733
-
-
Komorowski, M.1
Zurauskiene, J.2
Stumpf, M.P.H.3
-
40
-
-
34249079154
-
Network motifs: Theory and experimental approaches
-
Alon U. 2007 Network motifs: Theory and experimental approaches. Nat. Rev. Genet. 8, 450-461. (doi:10.1038/nrg2102).
-
(2007)
Nat. Rev. Genet.
, vol.8
, pp. 450-461
-
-
Alon, U.1
-
41
-
-
33745780500
-
Network motifs: Structure does not determine function
-
Ingram P, Stumpf MPH, Stark J. 2006 Network motifs: structure does not determine function. BMC Genomics 7, 108. (doi:10.1186/1471-2164-7-108).
-
(2006)
BMC Genomics
, vol.7
, pp. 108
-
-
Ingram, P.1
Stumpf, M.P.H.2
Stark, J.3
-
42
-
-
77952904483
-
Statistical model comparison applied to common network motifs
-
Domedel-Puig N, Pournara I, Wernisch L. 2010 Statistical model comparison applied to common network motifs. BMC Syst. Biol. 4, 18. (doi:10.1186/1752-0509-4-18).
-
(2010)
BMC Syst. Biol
, vol.4
, pp. 18
-
-
Domedel-Puig, N.1
Pournara, I.2
Wernisch, L.3
-
43
-
-
55749111058
-
Linear motif atlas for phosphorylation-dependent signaling
-
Miller ML et al. 2008 Linear motif atlas for phosphorylation-dependent signaling. Sci. Signal. 1, ra2. (doi:10.1126/scisignal.1159433).
-
(2008)
Sci. Signal. 1, Ra2.
-
-
Miller, M.L.1
-
44
-
-
0142027814
-
Structure and function of the feed-forward loop network motif
-
Mangan S, Alon U. 2003 Structure and function of the feed-forward loop network motif. Proc. Natl Acad. Sci. USA 100, 11980-11985. (doi:10.1073/pnas.2133841100).
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 11980-11985
-
-
Mangan, S.1
Alon, U.2
-
45
-
-
0037119587
-
Stochastic gene expression in a single cell
-
New York N.Y
-
Elowitz MB, Levine AJ, Siggia ED, Swain PS. 2002 Stochastic gene expression in a single cell. Science (New York N.Y.) 297, 1183-1186. (doi:10.1126/science.1070919).
-
(2002)
Science
, vol.297
, pp. 1183-1186
-
-
Elowitz, M.B.1
Levine, A.J.2
Siggia, E.D.3
Swain, P.S.4
-
46
-
-
55449126379
-
Nonidentifiability of the source of intrinsic noise in gene expression from single-burst data
-
Ingram P, Stumpf MPH, Stark J. 2008 Nonidentifiability of the source of intrinsic noise in gene expression from single-burst data. PLoS Comput. Biol. 4, e1000192. (doi:10.1371/journal.pcbi.1000192).
-
(2008)
PLoS Comput. Biol.
, vol.4
, pp. e1000192
-
-
Ingram, P.1
Stumpf, M.P.H.2
Stark, J.3
-
47
-
-
33645027986
-
Stochastic protein expression in individual cells at the single molecule level
-
Cai L, Friedman N, Xie XS. 2006 Stochastic protein expression in individual cells at the single molecule level. Nature 440, 358-362. (doi:10.1038/nature04599).
-
(2006)
Nature
, vol.440
, pp. 358-362
-
-
Cai, L.1
Friedman, N.2
Xie, X.S.3
-
48
-
-
33750247101
-
Linking stochastic dynamics to population distribution: An analytical framework of gene expression
-
Friedman N, Cai L, Xie XS. 2006 Linking stochastic dynamics to population distribution: An analytical framework of gene expression. Phys. Rev. Lett. 97, 168302. (doi:10.1103/PhysRevLett.97.168302).
-
(2006)
Phys. Rev. Lett.
, vol.97
, pp. 168302
-
-
Friedman, N.1
Cai, L.2
Xie, X.S.3
|