-
1
-
-
70449375094
-
Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics
-
Äijö T, Lähdesmäki H (2009) Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics. Bioinformatics 25(22): 2937-2944.
-
(2009)
Bioinformatics
, vol.25
, Issue.22
, pp. 2937-2944
-
-
Äijö, T.1
Lähdesmäki, H.2
-
2
-
-
52949109243
-
Algorithms for inference, analysis and control of boolean networks
-
In: Horimoto K, Regensburger G, Rosenkranz M, Yoshida H (eds), Springer, Berlin
-
Akutsu T, Hayashida M, Tamura T (2008) Algorithms for inference, analysis and control of boolean networks. In: Horimoto K, Regensburger G, Rosenkranz M, Yoshida H (eds) Algebraic biology. Lecture Notes in computer science, vol 5147. Springer, Berlin, pp 1-15.
-
(2008)
Algebraic biology. Lecture Notes in computer science
, vol.5147
, pp. 1-15
-
-
Akutsu, T.1
Hayashida, M.2
Tamura, T.3
-
3
-
-
0034721164
-
Error and attack tolerance of complex networks
-
Albert R, Jeong H, Barabasi AL (2000) Error and attack tolerance of complex networks. Nature 406: 378-382.
-
(2000)
Nature
, vol.406
, pp. 378-382
-
-
Albert, R.1
Jeong, H.2
Barabasi, A.L.3
-
4
-
-
84868160004
-
Diverse control of metabolism and other cellular processes in streptomyces coelicolor by the phop transcription factor: genome-wide identification of in vivo targets
-
Allenby NEE, Laing E, Bucca G, Kierzek AM, Smith CP (2012) Diverse control of metabolism and other cellular processes in streptomyces coelicolor by the phop transcription factor: genome-wide identification of in vivo targets. Nucleic Acids Res 40(19): 9543-9556.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.19
, pp. 9543-9556
-
-
Allenby, N.E.E.1
Laing, E.2
Bucca, G.3
Kierzek, A.M.4
Smith, C.P.5
-
6
-
-
34249079154
-
Network motifs: theory and experimental approaches
-
Alon U (2007) Network motifs: theory and experimental approaches. Nat Rev Genet 8: 450-461.
-
(2007)
Nat. Rev. Genet.
, vol.8
, pp. 450-461
-
-
Alon, U.1
-
7
-
-
24344505520
-
A mopso algorithm based exclusively on pareto dominance concepts
-
EMO 2005, Springer, Berlin
-
Alvarez-benitez JE, Everson RM, Fieldsend JE (2005) A mopso algorithm based exclusively on pareto dominance concepts. In: Proceedings of the third international conference on evolutionary multicriterion optimization, EMO 2005, Springer, Berlin, pp 459-473.
-
(2005)
Proceedings of the third international conference on evolutionary multicriterion optimization
, pp. 459-473
-
-
Alvarez-benitez, J.E.1
Everson, R.M.2
Fieldsend, J.E.3
-
9
-
-
2942606066
-
Structure and evolution of transcriptional regulatory networks
-
Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA (2004) Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol 14(3): 283-291.
-
(2004)
Curr Opin Struct Biol
, vol.14
, Issue.3
, pp. 283-291
-
-
Babu, M.M.1
Luscombe, N.M.2
Aravind, L.3
Gerstein, M.4
Teichmann, S.A.5
-
10
-
-
79953824573
-
Automated innovization for simultaneous discovery of multiple rules in bi-objective problems
-
R. Takahashi, K. Deb, E. Wanner, and S. Greco (Eds.), Berlin: Springer
-
Bandaru S, Deb K (2011) Automated innovization for simultaneous discovery of multiple rules in bi-objective problems. In: Takahashi R, Deb K, Wanner E, Greco S (eds) Evolutionary multi-criterion optimization. Lecture Notes in computer science, vol 6576, Springer, Berlin, pp 1-15.
-
(2011)
Evolutionary Multi-Criterion Optimization, Lecture Notes in Computer Science, Vol. 6576
, pp. 1-15
-
-
Bandaru, S.1
Deb, K.2
-
11
-
-
84860388963
-
Towards automating the discovery of certain innovative design principles through a clustering-based optimization technique
-
Bandaru S, Deb K (2011) Towards automating the discovery of certain innovative design principles through a clustering-based optimization technique. Eng Optim 43(9): 911-941.
-
(2011)
Engineering Optimization
, vol.43
, Issue.9
, pp. 911-941
-
-
Bandaru, S.1
Deb, K.2
-
12
-
-
84875501275
-
A dimensionally-aware genetic programming architecture for automated innovization
-
R. Purshouse, P. Fleming, C. Fonseca, S. Greco, and J. Shaw (Eds.), Berlin Heidelberg: Springer
-
Bandaru S, Deb K (2013) A dimensionally-aware genetic programming architecture for automated innovization. In: Purshouse R, Fleming P, Fonseca C, Greco S, Shaw J (eds) Evolutionary multi-criterion optimization. Lecture Notes in computer science, vol 7811, Springer, Berlin, pp 513-527.
-
(2013)
Evolutionary Multi-Criterion Optimization, Lecture Notes in Computer Science, Vol. 7811
, pp. 513-527
-
-
Bandaru, S.1
Deb, K.2
-
13
-
-
33847055114
-
How to infer gene networks from expression profiles
-
Bansal M, Belcastro V, Ambesi-Impiombato A, di Bernardo D (2007) How to infer gene networks from expression profiles. Mol Syst Biol 3(78): 1-10.
-
(2007)
Mol Syst Biol
, vol.3
, Issue.78
, pp. 1-10
-
-
Bansal, M.1
Belcastro, V.2
Ambesi-Impiombato, A.3
di Bernardo, D.4
-
14
-
-
33645307955
-
Inference of gene regulatory networks and compound mode of action from time course gene expression profiles
-
Bansal M, Gatta GD, di Bernardo D (2006) Inference of gene regulatory networks and compound mode of action from time course gene expression profiles. Bioinformatics 22(7): 815-822.
-
(2006)
Bioinformatics
, vol.22
, Issue.7
, pp. 815-822
-
-
Bansal, M.1
Gatta, G.D.2
di Bernardo, D.3
-
15
-
-
13844253637
-
A bayesian approach to reconstructing genetic regulatory networks with hidden factors
-
Beal MJ, Falciani F, Ghahramani Z, Rangel C, Wild DL (2005) A bayesian approach to reconstructing genetic regulatory networks with hidden factors. Bioinformatics 21(3): 349-356.
-
(2005)
Bioinformatics
, vol.21
, Issue.3
, pp. 349-356
-
-
Beal, M.J.1
Falciani, F.2
Ghahramani, Z.3
Rangel, C.4
Wild, D.L.5
-
16
-
-
0242321034
-
Artificial life: organization, adaptation and complexity from the bottom up
-
Bedau MA (2003) Artificial life: organization, adaptation and complexity from the bottom up. Trends Cogn Sci 7(11): 505-512.
-
(2003)
Trends in Cognitive Sciences
, vol.7
, Issue.11
, pp. 505-512
-
-
Bedau, M.A.1
-
19
-
-
21444452397
-
Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks
-
di Bernardo D, Thompson MJ, Gardner TS, Chobot SE, Eastwood EL, Wojtovich AP, Elliott SJ, Schaus SE, Collins JJ (2005) Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nat Biotechnol (3): 377-383.
-
(2005)
Nat Biotechnol
, Issue.3
, pp. 377-383
-
-
di Bernardo, D.1
Thompson, M.J.2
Gardner, T.S.3
Chobot, S.E.4
Eastwood, E.L.5
Wojtovich, A.P.6
Elliott, S.J.7
Schaus, S.E.8
Collins, J.J.9
-
20
-
-
0037592480
-
Evolution strategies a comprehensive introduction
-
Beyer HG, Schwefel HP (2002) Evolution strategies a comprehensive introduction. Nat Comput 1(1): 3-52.
-
(2002)
Nat Comput
, vol.1
, Issue.1
, pp. 3-52
-
-
Beyer, H.G.1
Schwefel, H.P.2
-
21
-
-
34548088935
-
Do additional objectives make a problem harder?
-
GECCO'07. ACM, New York, NY, USA
-
Brockhoff D, Friedrich T, Hebbinghaus N, Klein C, Neumann F, Zitzler E (2007) Do additional objectives make a problem harder? In: Proceedings of the 9th annual conference on Genetic and evolutionary computation, GECCO'07. ACM, New York, NY, USA, pp 765-772.
-
(2007)
Proceedings of the 9th annual conference on Genetic and evolutionary computation
, pp. 765-772
-
-
Brockhoff, D.1
Friedrich, T.2
Hebbinghaus, N.3
Klein, C.4
Neumann, F.5
Zitzler, E.6
-
22
-
-
67650132402
-
On the effects of adding objectives to plateau functions
-
Brockhoff D, Friedrich T, Hebbinghaus N, Klein C, Neumann F, Zitzler E (2009) On the effects of adding objectives to plateau functions. Evol Comput IEEE Trans 13(3): 591-603.
-
(2009)
Evolutionary Computation, IEEE Transactions on
, vol.13
, Issue.3
, pp. 591-603
-
-
Brockhoff, D.1
Friedrich, T.2
Hebbinghaus, N.3
Klein, C.4
Neumann, F.5
Zitzler, E.6
-
25
-
-
67649238145
-
Simultaneous structure discovery and parameter estimation in gene networks using a multi-objective gp-pso hybrid approach
-
Cai X, Koduru P, Das S, Welch SM (2009) Simultaneous structure discovery and parameter estimation in gene networks using a multi-objective gp-pso hybrid approach. Int J Bioinform Res Appl 5(3): 254-268.
-
(2009)
Int J Bioinf Res Appl
, vol.5
, Issue.3
, pp. 254-268
-
-
Cai, X.1
Koduru, P.2
Das, S.3
Welch, S.M.4
-
27
-
-
84894376059
-
Computational systems biology on networks and dynamics
-
World Publishing Corporation
-
Chen L (2007) Computational systems biology on networks and dynamics. In: Optimization and systems biology. Lecture notes in operations research, vol 7. World Publishing Corporation, pp 5-12. http://www. aporc. org/LNOR/7/OSB2007F02. pdf.
-
(2007)
Optimization and systems biology. Lecture notes in operations research
, vol.7
, pp. 5-12
-
-
Chen, L.1
-
28
-
-
33745622668
-
An effective structure learning method for constructing gene networks
-
Chen Xw, Anantha G, Wang X (2006) An effective structure learning method for constructing gene networks. Bioinformatics 22(11): 1367-1374.
-
(2006)
Bioinformatics
, vol.22
, Issue.11
, pp. 1367-1374
-
-
Chen, X.1
Anantha, G.2
Wang, X.3
-
30
-
-
84869054145
-
On the reconstruction of genetic network from partial microarray data
-
T. Huang, Z. Zeng, C. Li, and C. Leung (Eds.), Berlin Heidelberg: Springer
-
Chowdhury A, Chetty M, Vinh X (2012) On the reconstruction of genetic network from partial microarray data. In: Huang T, Zeng Z, Li C, Leung C (eds) Neural information processing. Lecture Notes in computer science, vol 7663. Springer, Berlin, pp 689-696.
-
(2012)
Neural Information Processing, Lecture Notes in Computer Science, Vol. 7663
, pp. 689-696
-
-
Chowdhury, A.1
Chetty, M.2
Vinh, X.3
-
31
-
-
48249134043
-
Evolution of evolvability in gene regulatory networks
-
e1000,112
-
Crombach A, Hogeweg P (2008) Evolution of evolvability in gene regulatory networks. PLoS Comput Biol 4(7): e1000112.
-
(2008)
PLoS Comput Biol
, vol.4
, Issue.7
-
-
Crombach, A.1
Hogeweg, P.2
-
32
-
-
0034644270
-
The segment polarity network is a robust developmental module
-
doi:10.1038/35018085
-
von Dassow G, Meir E, Munro EM, Odell GM (2000) The segment polarity network is a robust developmental module. Nature 406: 188-192. doi: 10. 1038/35018085.
-
(2000)
Nature
, vol.406
, pp. 188-192
-
-
von Dassow, G.1
Meir, E.2
Munro, E.M.3
Odell, G.M.4
-
33
-
-
12344321571
-
Discovery of meaningful associations in genomic data using partial correlation coefficients
-
DeLa Fuente A, Bing N, Hoeschele I, Mendes P (2004) Discovery of meaningful associations in genomic data using partial correlation coefficients. Bioinformatics 20(18): 3565-3574.
-
(2004)
Bioinformatics
, vol.20
, Issue.18
, pp. 3565-3574
-
-
Dela Fuente, A.1
Bing, N.2
Hoeschele, I.3
Mendes, P.4
-
35
-
-
0036530772
-
A fast and elitist multiobjective genetic algorithm: Nsga-ii
-
Deb K, Pratap A, Agarwal S, Meyarivan T (2002) A fast and elitist multiobjective genetic algorithm: nsga-ii. Evol Comput IEEE Trans 6(2): 182-197.
-
(2002)
Evolutionary Computation, IEEE Transactions on
, vol.6
, Issue.2
, pp. 182-197
-
-
Deb, K.1
Pratap, A.2
Agarwal, S.3
Meyarivan, T.4
-
36
-
-
33750258231
-
Innovization: innovating design principles through optimization
-
GECCO'06. ACM, New York, NY, USA
-
Deb K, Srinivasan A (2006) Innovization: innovating design principles through optimization. In: Proceedings of the 8th annual conference on genetic and evolutionary computation, GECCO'06. ACM, New York, NY, USA, pp 1629-1636.
-
(2006)
Proceedings of the 8th annual conference on genetic and evolutionary computation
, pp. 1629-1636
-
-
Deb, K.1
Srinivasan, A.2
-
41
-
-
77954023542
-
Comparison of exact static and dynamic bayesian context inference methods for activity recognition
-
IEEE
-
Frank K, Rckl M, Nadales MJV, Robertson P, Pfeifer T (2010) Comparison of exact static and dynamic bayesian context inference methods for activity recognition. In: PerCom workshops. IEEE, pp 189-195.
-
(2010)
PerCom workshops
, pp. 189-195
-
-
Frank, K.1
Rckl, M.2
Nadales, M.J.V.3
Robertson, P.4
Pfeifer, T.5
-
43
-
-
0038048325
-
Inferring genetic networks and identifying compound mode of action via expression profiling
-
Gardner TS, di Bernardo D, Lorenz D, Collins JJ (2003) Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301(5629): 102-105.
-
(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
-
-
34548538013
-
Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge
-
Geier F, Timmer J, Fleck C (2007) Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge. BMC Syst Biol 1.
-
(2007)
BMC Syst Biol
, vol.1
-
-
Geier, F.1
Timmer, J.2
Fleck, C.3
-
45
-
-
84894327478
-
-
GenBank: National center for biotechnology information, genetic sequence data bank (June 15 2013)
-
GenBank: National center for biotechnology information, genetic sequence data bank (June 15 2013). ftp://ftp. ncbi. nih. gov/genbank/gbrel. txt.
-
-
-
-
46
-
-
70649104601
-
Coupling oscillations and switches in genetic networks
-
Gonze D (2010) Coupling oscillations and switches in genetic networks. Biosystems 99(1): 60-69.
-
(2010)
Biosystems
, vol.99
, Issue.1
, pp. 60-69
-
-
Gonze, D.1
-
49
-
-
84887667705
-
Borg: An auto-adaptive many-objective evolutionary computing framework
-
Hadka D, Reed P (2013) Borg: An auto-adaptive many-objective evolutionary computing framework. Evol Comput 21: 231-259.
-
(2013)
Evolutionary Computation
, vol.21
, pp. 231-259
-
-
Hadka, D.1
Reed, P.2
-
54
-
-
84875990816
-
Differential expression analysis for pathways
-
e1002,967
-
Haynes WA, Higdon R, Stanberry L, Collins D, Kolker E (2013) Differential expression analysis for pathways. PLoS Comput Biol 9(3): e1002967.
-
(2013)
PLoS Comput Biol
, vol.9
, Issue.3
-
-
Haynes, W.A.1
Higdon, R.2
Stanberry, L.3
Collins, D.4
Kolker, E.5
-
55
-
-
61349180117
-
Gene regulatory network inference: Data integration in dynamic modelsa review
-
Hecker M, Lambeck S, Toepfer S, van Someren E, Guthke R (2009) Gene regulatory network inference: data integration in dynamic modelsa review. Biosystems 96(1): 86-103.
-
(2009)
Biosystems
, vol.96
, Issue.1
, pp. 86-103
-
-
Hecker, M.1
Lambeck, S.2
Toepfer, S.3
van Someren, E.4
Guthke, R.5
-
56
-
-
77953207828
-
-
1st edn. Microsoft Research, Redmond, Washington
-
Hey T, Tansley S, Tolle K (eds) (2009) The fourth paradigm: data-intensive scientific discovery, 1st edn. Microsoft Research, Redmond, Washington.
-
(2009)
The fourth paradigm: Data-intensive scientific discovery
-
-
Hey, T.1
Tansley, S.2
Tolle, K.3
-
58
-
-
84864386279
-
Multi-criteria optimization of regulation in metabolic networks
-
e41,122
-
Higuera C, Villaverde AF, Banga JR, Ross J, Morn F (2012) Multi-criteria optimization of regulation in metabolic networks. PLoS ONE 7(7): e41122.
-
(2012)
PLoS ONE
, vol.7
, Issue.7
-
-
Higuera, C.1
Villaverde, A.F.2
Banga, J.R.3
Ross, J.4
Morn, F.5
-
59
-
-
72749125592
-
Multiobjectivization for parameter estimation: a case-study on the segment polarity network of drosophila
-
In: Rothlauf F et al (eds), ACM, New York, NY, USA
-
Hohm T, Zitzler, E (2009) Multiobjectivization for parameter estimation: a case-study on the segment polarity network of drosophila. In: Rothlauf F et al (eds) GECCO'09: genetic and evolutionary computation conference (GECCO 2009). ACM, New York, NY, USA, pp 209-216.
-
(2009)
GECCO'09: Genetic and evolutionary computation conference (GECCO 2009)
, pp. 209-216
-
-
Hohm, T.1
Zitzler, E.2
-
60
-
-
0043130707
-
Inferring gene regulatory networks from time-ordered gene expression data of bacillus subtilis using differential equations
-
Hoon MD, Imoto S, Miyano S (2003) Inferring gene regulatory networks from time-ordered gene expression data of bacillus subtilis using differential equations. In: Proceedings of the pacific symposium on biocomputing, pp 17-28.
-
(2003)
Proceedings of the pacific symposium on biocomputing
, pp. 17-28
-
-
Hoon, M.D.1
Imoto, S.2
Miyano, S.3
-
61
-
-
84901435615
-
Exploring regenerative mechanisms found in flatworms by artificial evolutionary techniques using genetic regulatory networks
-
Hotz PE (2003) Exploring regenerative mechanisms found in flatworms by artificial evolutionary techniques using genetic regulatory networks. In: Proceedings of the congress on evolutionary computation, 2003. CEC'03, vol 3. pp 2026-2033.
-
(2003)
Proceedings of the congress on evolutionary computation, 2003. CEC'03
, vol.3
, pp. 2026-2033
-
-
Hotz, P.E.1
-
62
-
-
55749085252
-
Solving large scale global optimization using improved particle swarm optimizer
-
(IEEE World Congress on Computational Intelligence)
-
Hsieh ST, Sun TY, Liu CC, Tsai SJ (2008) Solving large scale global optimization using improved particle swarm optimizer. In: Proceedings of the IEEE congress on evolutionary computation, 2008. CEC 2008. (IEEE World Congress on Computational Intelligence), pp 1777-1784.
-
(2008)
Proceedings of the IEEE congress on evolutionary computation, 2008. CEC 2008
, pp. 1777-1784
-
-
Hsieh, S.T.1
Sun, T.Y.2
Liu, C.C.3
Tsai, S.J.4
-
63
-
-
0036749274
-
Inference of a gene regulatory network by means of interactive evolutionary computing
-
Iba H, Mimura A (2002) Inference of a gene regulatory network by means of interactive evolutionary computing. Inf Sci Inf Comput Sci 145(3-4): 225-236.
-
(2002)
Inf. Sci. Inf. Comput. Sci.
, vol.145
, Issue.3-4
, pp. 225-236
-
-
Iba, H.1
Mimura, A.2
-
64
-
-
84876041347
-
-
(3/7/13)
-
IBM: What is big data? (3/7/13). http://www-01. ibm. com/software/data/bigdata/.
-
IBM: What is big data?
-
-
-
65
-
-
33745780500
-
Network motifs: structure does not determine function
-
Ingram P, Stumpf M, Stark J (2006) Network motifs: structure does not determine function. BMC Genomics 7(1): 1-12.
-
(2006)
BMC Genomics
, vol.7
, Issue.1
, pp. 1-12
-
-
Ingram, P.1
Stumpf, M.2
Stark, J.3
-
67
-
-
84875485202
-
An improved adaptive approach for elitist nondominated sorting genetic algorithm for many-objective optimization
-
In: Purshouse R, Fleming P, Fonseca C, Greco S, Shaw J (eds), Springer, Berlin
-
Jain H, Deb K (2013) An improved adaptive approach for elitist nondominated sorting genetic algorithm for many-objective optimization. In: Purshouse R, Fleming P, Fonseca C, Greco S, Shaw J (eds) Evolutionary multi-criterion optimization, Lecture Notes in computer science, vol 7811. Springer, Berlin, pp 307-321.
-
(2013)
Evolutionary multi-criterion optimization, Lecture Notes in computer science
, vol.7811
, pp. 307-321
-
-
Jain, H.1
Deb, K.2
-
68
-
-
20944439075
-
Helper-objectives: Using multi-objective evolutionary algorithms for single-objective optimisation
-
Jensen MT (2004) Helper-objectives: using multi-objective evolutionary algorithms for single-objective optimisation. J Math Model Algorithms 3: 323-347.
-
(2004)
Journal of Mathematical Modelling and Algorithms
, vol.3
, pp. 323-347
-
-
Jensen, M.T.1
-
71
-
-
78650198665
-
Emergence of robust regulatory motifs from in silico evolution of sustained oscillation
-
Jin Y, Meng Y (2011) Emergence of robust regulatory motifs from in silico evolution of sustained oscillation. Biosystems 103(1): 38-44.
-
(2011)
Biosystems
, vol.103
, Issue.1
, pp. 38-44
-
-
Jin, Y.1
Meng, Y.2
-
72
-
-
0036207347
-
Modeling and simulation of genetic regulatory systems: A literature review
-
de Jong H (2002) Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol 9: 67-103.
-
(2002)
J Comput Biol
, vol.9
, pp. 67-103
-
-
de Jong, H.1
-
73
-
-
84873667710
-
Modeling and simulation of genetic regulatory networks by ordinary differential equations
-
Hindawi Publishing Corporation, New York
-
de Jong H, Geiselmann J (2005) Modeling and simulation of genetic regulatory networks by ordinary differential equations. In: Genomic signal processing and statistics. Hindawi Publishing Corporation, New York, pp 201-239.
-
(2005)
Genomic signal processing and statistics
, pp. 201-239
-
-
de Jong, H.1
Geiselmann, J.2
-
74
-
-
75149166629
-
Reverse engineering gene regulatory network from microarray data using linear time-variant model
-
Kabir M, Noman N, Iba H (2010) Reverse engineering gene regulatory network from microarray data using linear time-variant model. BMC Bioinform 11: S56.
-
(2010)
BMC Bioinformatics
, vol.11
-
-
Kabir, M.1
Noman, N.2
Iba, H.3
-
75
-
-
52649087274
-
Modelling and analysis of gene regulatory networks
-
Karlebach G, Shamir R (2008) Modelling and analysis of gene regulatory networks. Nat Rev Mol Cell Biol 9: 770-780.
-
(2008)
Nat Rev Mol Cell Biol
, vol.9
, pp. 770-780
-
-
Karlebach, G.1
Shamir, R.2
-
77
-
-
41849102778
-
Reverse engineering: the architecture of biological networks
-
Khammash M (2008) Reverse engineering: the architecture of biological networks. Biotechniques 44: 323-329.
-
(2008)
Biotechniques
, vol.44
, pp. 323-329
-
-
Khammash, M.1
-
78
-
-
3442884234
-
Systems biology: from physiology to gene regulation
-
Khammash M, El-Samad H (2004) Systems biology: from physiology to gene regulation. Control Syst IEEE 24(4): 62-76.
-
(2004)
Control Systems, IEEE
, vol.24
, Issue.4
, pp. 62-76
-
-
Khammash, M.1
El-Samad, H.2
-
79
-
-
0037461033
-
Dynamic modeling of genetic networks using genetic algorithm and s-system
-
Kikuchi S, Tominaga D, Arita M, Takahashi K, Tomita M (2003) Dynamic modeling of genetic networks using genetic algorithm and s-system. Bioinformatics 19(5): 643-650.
-
(2003)
Bioinformatics
, vol.19
, Issue.5
, pp. 643-650
-
-
Kikuchi, S.1
Tominaga, D.2
Arita, M.3
Takahashi, K.4
Tomita, M.5
-
80
-
-
0037079054
-
Computational systems biology
-
Kitano H (2002) Computational systems biology. Nature 420: 206-210.
-
(2002)
Nature
, vol.420
, pp. 206-210
-
-
Kitano, H.1
-
82
-
-
79952112403
-
Genetic algorithms and their application to in silico evolution of genetic regulatory networks
-
D. Fenyö (Ed.), New York City: Humana Press
-
Knabe JF, Wegner K, Nehaniv CL, Schilstra MJ (2010) Genetic algorithms and their application to in silico evolution of genetic regulatory networks. In: Fenyö D (eds) Computational biology, methods in molecular biology, vol 673, Humana Press, New York City, pp 297-321.
-
(2010)
Computational Biology, Methods in Molecular Biology, Vol. 673
, pp. 297-321
-
-
Knabe, J.F.1
Wegner, K.2
Nehaniv, C.L.3
Schilstra, M.J.4
-
83
-
-
0034199912
-
Approximating the nondominated front using the pareto archived evolution strategy
-
Knowles JD, Corne DW (2000) Approximating the nondominated front using the pareto archived evolution strategy. Evol Comput 8(2): 149-172.
-
(2000)
Evol. Comput.
, vol.8
, Issue.2
, pp. 149-172
-
-
Knowles, J.D.1
Corne, D.W.2
-
84
-
-
84931320658
-
Reducing local optima in single-objective problems by multi-objectivization
-
EMO'01. Springer, London
-
Knowles JD, Watson RA, Corne D (2001) Reducing local optima in single-objective problems by multi-objectivization. In: Proceedings of the first international conference on evolutionary multi-criterion optimization, EMO'01. Springer, London, pp 269-283.
-
(2001)
Proceedings of the first international conference on evolutionary multi-criterion optimization
, pp. 269-283
-
-
Knowles, J.D.1
Watson, R.A.2
Corne, D.3
-
86
-
-
33746922321
-
Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergence
-
Kuo PD, Banzhaf W, Leier A (2006) Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergence. Biosystems 85(3): 177-200.
-
(2006)
Biosystems
, vol.85
, Issue.3
, pp. 177-200
-
-
Kuo, P.D.1
Banzhaf, W.2
Leier, A.3
-
87
-
-
39749099388
-
Analysis of feedback loops and robustness in network evolution based on boolean models
-
doi: 10. 1186/1471-2105-8-430
-
Kwon YK, Cho KH (2007) Analysis of feedback loops and robustness in network evolution based on boolean models. BMC Bioinform 430. doi: 10. 1186/1471-2105-8-430.
-
(2007)
BMC Bioinform
, vol.430
-
-
Kwon, Y.K.1
Cho, K.H.2
-
88
-
-
41349112310
-
Quantitative analysis of robustness and fragility in biological networks based on feedback dynamics
-
Kwon YK, Cho KH (2008) Quantitative analysis of robustness and fragility in biological networks based on feedback dynamics. Bioinformatics 24(7).
-
(2008)
Bioinformatics
, vol.24
, Issue.7
-
-
Kwon, Y.K.1
Cho, K.H.2
-
90
-
-
79953021881
-
-
1st edn., chap. Multicore computing and scientific discovery. Microsoft Research, Redmond, Washington
-
Larus J, Gannon D (2009) The fourth paradigm: data-intensive scientific discovery, 1st edn., chap. Multicore computing and scientific discovery. Microsoft Research, Redmond, Washington, pp 125-129.
-
(2009)
The fourth paradigm: data-intensive scientific discovery
, pp. 125-129
-
-
Larus, J.1
Gannon, D.2
-
91
-
-
84878544540
-
A spatial predator-prey approach to multi-objective optimization: a preliminary study
-
PPSN V. Springer, London
-
Laumanns M, Rudolph G, Schwefel HP (1998) A spatial predator-prey approach to multi-objective optimization: a preliminary study. In: Proceedings of the 5th international conference on parallel problem solving from nature, PPSN V. Springer, London, pp 241-249.
-
(1998)
Proceedings of the 5th international conference on parallel problem solving from nature
, pp. 241-249
-
-
Laumanns, M.1
Rudolph, G.2
Schwefel, H.P.3
-
93
-
-
84872827093
-
Survival of the sparsest: robust gene networks are parsimonious
-
Leclerc RD (2008) Survival of the sparsest: robust gene networks are parsimonious. Mol Syst Biol 1-6.
-
(2008)
Mol Syst Biol
, pp. 1-6
-
-
Leclerc, R.D.1
-
94
-
-
84894326449
-
Inferring gene regulatory networks by incremental evolution and network decomposition
-
World Publishing Corporation
-
Lee W-P, Hsiao Y-T (2008) Inferring gene regulatory networks by incremental evolution and network decomposition. In: Optimization and systems biology. Lecture notes in operations research, vol 9. World Publishing Corporation, pp 311-324. http://www. aporc. org/LNOR/9/OSB2008F40. pdf.
-
(2008)
Optimization and systems biology. Lecture notes in operations research
, vol.9
, pp. 311-324
-
-
Lee, W.-P.1
Hsiao, Y.-T.2
-
95
-
-
38049033443
-
Towards evolutionary network reconstruction tools for systems biology
-
E. Marchiori, J. Moore, and J. Rajapakse (Eds.), Berlin Heidelberg: Springer
-
Lenser T, Hinze T, Ibrahim B, Dittrich P (2007) Towards evolutionary network reconstruction tools for systems biology. In: Marchiori E, Moore J, Rajapakse J (eds) Evolutionary computation, machine learning and data mining in bioinformatics. Lecture Notes in computer science, vol 4447, Springer, Berlin, pp 132-142.
-
(2007)
Evolutionary Computation,Machine Learning and Data Mining in Bioinformatics. Lecture Notes in Computer Science, Vol. 4447
, pp. 132-142
-
-
Lenser, T.1
Hinze, T.2
Ibrahim, B.3
Dittrich, P.4
-
96
-
-
85032751721
-
A systems biology perspective on signal processing in genetic network motifs [life sciences]
-
Li C, Chen L, Aihara K (2007) A systems biology perspective on signal processing in genetic network motifs [life sciences]. Signal Process Mag IEEE 24(2): 136-147.
-
(2007)
Signal Processing Magazine, IEEE
, vol.24
, Issue.2
, pp. 136-147
-
-
Li, C.1
Chen, L.2
Aihara, K.3
-
97
-
-
84894359363
-
An optimization model for gene regulatory network reconstruction with known biological information
-
World Publishing Corporation
-
Li J, Zhang X-S (2007) An optimization model for gene regulatory network reconstruction with known biological information. In: Optimization and systems biology. Lecture notes in operations research, vol 7. World Publishing Corporation, pp 35-44. http://www. aporc. org/LNOR/7/OSB2007F06. pdf.
-
(2007)
Optimization and systems biology. Lecture notes in operations research
, vol.7
, pp. 35-44
-
-
Li, J.1
Zhang, X.-S.2
-
98
-
-
84859719176
-
Cooperatively coevolving particle swarms for large scale optimization
-
Li X, Yao X (2012) Cooperatively coevolving particle swarms for large scale optimization. Evol Comput IEEE Trans 16(2): 210-224.
-
(2012)
Evolutionary Computation, IEEE Transactions on
, vol.16
, Issue.2
, pp. 210-224
-
-
Li, X.1
Yao, X.2
-
99
-
-
80052064627
-
Temporal graphical models for cross-species gene regulatory network discovery
-
Liu Y, Niculescu-Mizil A, Lozano AC, Lu Y (2011) Temporal graphical models for cross-species gene regulatory network discovery. J Bioinform Comput Biol 9(2): 231-250.
-
(2011)
J. Bioinformatics and Computational Biology
, vol.9
, Issue.2
, pp. 231-250
-
-
Liu, Y.1
Niculescu-Mizil, A.2
Lozano, A.C.3
Lu, Y.4
-
101
-
-
0035221090
-
Development of a system for the inference of large scale genetic networks
-
Maki Y, Tominaga D, Okamoto M, Watanabe S, Eguchi Y (2001) Development of a system for the inference of large scale genetic networks. Pac Symp Biocomput 446-458.
-
(2001)
Pac Symp Biocomput
, pp. 446-458
-
-
Maki, Y.1
Tominaga, D.2
Okamoto, M.3
Watanabe, S.4
Eguchi, Y.5
-
102
-
-
33947305781
-
ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
-
Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Favera RD, Califano A (2006) ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinform 7(Suppl 1): S7.
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.SUPPL. 1
-
-
Margolin, A.A.1
Nemenman, I.2
Basso, K.3
Wiggins, C.4
Stolovitzky, G.5
Favera, R.D.6
Califano, A.7
-
103
-
-
84878979335
-
Biology: The big challenges of big data
-
Marx V (2013) Biology: The big challenges of big data. Nature 498: 255-260.
-
(2013)
Nature
, vol.498
, pp. 255-260
-
-
Marx, V.1
-
105
-
-
84860415026
-
Evolving random boolean networks with genetic algorithms for regulatory networks reconstruction
-
GECCO'11. ACM, New York, NY, USA
-
Mendoza MR, Bazzan ALC (2011) Evolving random boolean networks with genetic algorithms for regulatory networks reconstruction. In: Proceedings of the 13th annual conference on genetic and evolutionary computation, GECCO'11. ACM, New York, NY, USA, pp 291-298.
-
(2011)
Proceedings of the 13th annual conference on genetic and evolutionary computation
, pp. 291-298
-
-
Mendoza, M.R.1
Bazzan, A.L.C.2
-
106
-
-
0037174670
-
Network motifs: Simple building blocks of complex networks
-
Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, net U (2002) Network motifs: simple building blocks of complex networks. Science 298(5594): 824-827.
-
(2002)
Science
, vol.298
, Issue.5594
, pp. 824-827
-
-
Milo, R.1
Shen-Orr, S.2
Itzkovitz, S.3
Kashtan, N.4
Chklovskii, D.5
Net, U.6
-
108
-
-
79952959461
-
Reconstruction of gene regulatory networks using differential evolution
-
(ICCIT), 2010
-
Mondal B, Sarkar A, Hasan M, Noman N (2010) Reconstruction of gene regulatory networks using differential evolution. In: Proceedings of the 13th international conference on computer and information technology (ICCIT), 2010, pp 440-445.
-
(2010)
Proceedings of the 13th international conference on computer and information technology
, pp. 440-445
-
-
Mondal, B.1
Sarkar, A.2
Hasan, M.3
Noman, N.4
-
109
-
-
84901454547
-
Finding multiple solutions based on an evolutionary algorithm for inference of genetic networks by s-system
-
CEC'03
-
Morishita R, Imade H, Ono l, Ono N, Okamoto M (2003) Finding multiple solutions based on an evolutionary algorithm for inference of genetic networks by s-system. In: The 2003 congress on evolutionary computation, 2003. CEC'03, vol 1. pp 615-622.
-
(2003)
The 2003 congress on evolutionary computation, 2003
, vol.1
, pp. 615-622
-
-
Morishita, R.1
Imade, H.2
Ono, L.3
Ono, N.4
Okamoto, M.5
-
110
-
-
82355170988
-
Inference of s-system models of gene regulatory networks using immune algorithm
-
Nakayama T, Seno S, Matsuda H (2011) Inference of s-system models of gene regulatory networks using immune algorithm. J Bioinform Comput Biol 9: 75-86.
-
(2011)
J Bioinform Comput Biol
, vol.9
, pp. 75-86
-
-
Nakayama, T.1
Seno, S.2
Matsuda, H.3
-
112
-
-
33750281420
-
Inference of genetic networks using s-system: information criteria for model selection
-
GECCO'06. ACM, New York, NY, USA
-
Noman N, Iba H (2006) Inference of genetic networks using s-system: information criteria for model selection. In: Proceedings of the 8th annual conference on Genetic and evolutionary computation, GECCO'06. ACM, New York, NY, USA, pp 263-270.
-
(2006)
Proceedings of the 8th annual conference on Genetic and evolutionary computation
, pp. 263-270
-
-
Noman, N.1
Iba, H.2
-
113
-
-
36248948496
-
Inferring gene regulatory networks using differential evolution with local search heuristics
-
Noman N, Iba H (2007) Inferring gene regulatory networks using differential evolution with local search heuristics. IEEE/ACM Trans Comput Biol Bioinform 4(4): 634-647.
-
(2007)
IEEE/ACM Trans. Comput. Biol. Bioinformatics
, vol.4
, Issue.4
, pp. 634-647
-
-
Noman, N.1
Iba, H.2
-
114
-
-
84864028167
-
Information theoretic methods for modeling of gene regulatory networks
-
Noor A, Serpedin E, Nounou M, Nounou H, Mohamed N, Chouchane L (2012) Information theoretic methods for modeling of gene regulatory networks. In: IEEE symposium on computational intelligence in bioinformatics and computational biology (CIBCB), 2012, pp 418-423.
-
(2012)
IEEE symposium on computational intelligence in bioinformatics and computational biology (CIBCB), 2012
, pp. 418-423
-
-
Noor, A.1
Serpedin, E.2
Nounou, M.3
Nounou, H.4
Mohamed, N.5
Chouchane, L.6
-
115
-
-
84873516738
-
Visual data mining of biological networks: one size does not fit all
-
e1002833
-
Pastrello C, Otasek D, Fortney K, Agapito G, Cannataro M, Shirdel E, Jurisica I (2013) Visual data mining of biological networks: one size does not fit all. PLoS Comput Biol 9(1): e1002833.
-
(2013)
PLoS Comput Biol
, vol.9
, Issue.1
-
-
Pastrello, C.1
Otasek, D.2
Fortney, K.3
Agapito, G.4
Cannataro, M.5
Shirdel, E.6
Jurisica, I.7
-
116
-
-
84859149116
-
How to infer gene networks from expression profiles, revisited
-
Penfold CA, Wild DL (2011) How to infer gene networks from expression profiles, revisited. Interface Focus 1(6): 857-870. http://rsfs. royalsocietypublishing. org/content/early/2011/07/26/rsfs. 2011. 0053. abstract.
-
(2011)
Interface Focus
, vol.1
, Issue.6
, pp. 857-870
-
-
Penfold, C.A.1
Wild, D.L.2
-
117
-
-
84894347976
-
7th international conference, emo 2013, sheffield, uk, march 19-22, 2013 proceedings
-
Springer, Berlin
-
Purshouse RC, Fleming PJ, Fonseca CM, Greco S, Shaw J (2013) 7th international conference, emo 2013, sheffield, uk, march 19-22, 2013 proceedings. In: Evolutionary multi-criterion optimization, vol 7811. Springer, Berlin.
-
(2013)
Evolutionary multi-criterion optimization
, vol.7811
-
-
Purshouse, R.C.1
Fleming, P.J.2
Fonseca, C.M.3
Greco, S.4
Shaw, J.5
-
118
-
-
0035375137
-
Computational analysis of microarray data
-
Quackenbush J (2001) Computational analysis of microarray data. Nat Rev Genet (6): 418-427.
-
(2001)
Nat Rev Genet
, Issue.6
, pp. 418-427
-
-
Quackenbush, J.1
-
119
-
-
77956630040
-
Symmetry in biology: from genetic code to stochastic gene regulation
-
Ramons AF, Innocentini G, Forger FM, Hornos JE (2010) Symmetry in biology: from genetic code to stochastic gene regulation. IET Syst Biol 4(5): 311-329.
-
(2010)
IET Syst Biol
, vol.4
, Issue.5
, pp. 311-329
-
-
Ramons, A.F.1
Innocentini, G.2
Forger, F.M.3
Hornos, J.E.4
-
120
-
-
3142744689
-
Modeling t-cell activation using gene expression profiling and state-space models
-
Rangel C, Angus J, Ghahramani Z, Lioumi M, Sotheran E, Gaiba A, Wild DL, Falciani F (2004) Modeling t-cell activation using gene expression profiling and state-space models. Bioinformatics 20(9): 1361-1372.
-
(2004)
Bioinformatics
, vol.20
, Issue.9
, pp. 1361-1372
-
-
Rangel, C.1
Angus, J.2
Ghahramani, Z.3
Lioumi, M.4
Sotheran, E.5
Gaiba, A.6
Wild, D.L.7
Falciani, F.8
-
121
-
-
84867979927
-
Reverse engineering gene regulatory networks using approximate bayesian computation
-
Rau A, Jaffrzic F, Foulley JL, Doerge R (2012) Reverse engineering gene regulatory networks using approximate bayesian computation. Stat Comput 22(6): 1257-1271.
-
(2012)
Statistics and Computing
, vol.22
, Issue.6
, pp. 1257-1271
-
-
Rau, A.1
Jaffrzic, F.2
Foulley, J.L.3
Doerge, R.4
-
122
-
-
56449130100
-
A simple modification in cma-es achieving linear time and space complexity
-
G. Rudolph, T. Jansen, S. Lucas, C. Poloni, and N. Beume (Eds.), Berlin Heidelberg: Springer
-
Ros R, Hansen N (2008) A simple modification in cma-es achieving linear time and space complexity. In: Rudolph G, Jansen T, Lucas S, Poloni C, Beume N (eds) Parallel problem solving from nature PPSN X. Lecture Notes in computer science, vol 5199. Springer, Berlin, pp 296-305.
-
(2008)
Parallel Problem Solving from Nature PPSN X, Lecture Notes in Computer Science, Vol. 5199
, pp. 296-305
-
-
Ros, R.1
Hansen, N.2
-
123
-
-
4344693709
-
Evolutionary inference of a biological network as differential equations by genetic programming
-
Sakamoto E, Iba H (2001) Evolutionary inference of a biological network as differential equations by genetic programming. Genome Inform 276-277.
-
(2001)
Genome Inform
, pp. 276-277
-
-
Sakamoto, E.1
Iba, H.2
-
125
-
-
0014658880
-
Biochemical systems analysis: Ii. the steady-state solutions for an n-pool system using a power-law approximation
-
Savageau MA (1969) Biochemical systems analysis: Ii. The steady-state solutions for an n-pool system using a power-law approximation. J Theor Biol 25: 370-379.
-
(1969)
J Theor Biol
, vol.25
, pp. 370-379
-
-
Savageau, M.A.1
-
126
-
-
15944364151
-
An empirical bayes approach to inferring large-scale gene association networks
-
Schäfer J, Strimmer K (2005) An empirical Bayes approach to inferring large-scale gene association networks. Bioinformatics 21(6): 754-764.
-
(2005)
Bioinformatics
, vol.21
, Issue.6
, pp. 754-764
-
-
Schäfer, J.1
Strimmer, K.2
-
127
-
-
38049095819
-
Bio-logic: gene expression and the laws of combinatorial logic
-
Schilstra MJ, Nehaniv CL (2008) Bio-logic: gene expression and the laws of combinatorial logic. Artif Life 14.
-
(2008)
Artif Life
, vol.14
-
-
Schilstra, M.J.1
Nehaniv, C.L.2
-
128
-
-
64249142111
-
Distilling free-form natural laws from experimental data
-
Schmidt M, Lipson H (2009) Distilling free-form natural laws from experimental data. Science 324(5923): 81-85.
-
(2009)
Science
, vol.324
, Issue.5923
, pp. 81-85
-
-
Schmidt, M.1
Lipson, H.2
-
129
-
-
85047687585
-
Evolution and analysis of genetic networks for stable cellular growth and regeneration
-
Schramm L, Jin Y, Sendhoff B (2012) Evolution and analysis of genetic networks for stable cellular growth and regeneration. Artif Life 18: 425-444.
-
(2012)
Artificial Life
, vol.18
, pp. 425-444
-
-
Schramm, L.1
Jin, Y.2
Sendhoff, B.3
-
131
-
-
74149089224
-
A MATLAB toolbox for granger causal connectivity analysis
-
Seth AK (2010) A MATLAB toolbox for granger causal connectivity analysis. J Neurosci Methods 186(2): 262-273.
-
(2010)
J Neurosci Methods
, vol.186
, Issue.2
, pp. 262-273
-
-
Seth, A.K.1
-
132
-
-
0036578795
-
Network motifs in the transcriptional regulations network of escherichia coli
-
Shen-Orr SS, Milo R, Mangan S, Alon U (2002) Network motifs in the transcriptional regulations 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
-
133
-
-
14944363706
-
Construction of genetic network using evolutionary algorithm and combined fitness function
-
Shin A, Iba H (2003) Construction of genetic network using evolutionary algorithm and combined fitness function. Genome Inform 14: 2003.
-
(2003)
Genome Inform
, vol.14
, pp. 2003
-
-
Shin, A.1
Iba, H.2
-
134
-
-
84865248233
-
Integrating heterogeneous gene expression data for gene regulatory network modelling
-
Sîrbu A, Ruskin H, Crane M (2012) Integrating heterogeneous gene expression data for gene regulatory network modelling. Theory Biosci 131(2): 95-102.
-
(2012)
Theory Biosci
, vol.131
, Issue.2
, pp. 95-102
-
-
Sîrbu, A.1
Ruskin, H.2
Crane, M.3
-
135
-
-
77649176945
-
Comparison of evolutionary algorithms in gene regulatory network model inference
-
Sirbu A, Ruskin HJ, Crane M (2010) Comparison of evolutionary algorithms in gene regulatory network model inference. BMC Bioinform 11: 59.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 59
-
-
Sirbu, A.1
Ruskin, H.J.2
Crane, M.3
-
136
-
-
78649755610
-
Cross-platform microarray data normalisation for regulatory network inference
-
e13,822
-
Sîrbu A, Ruskin HJ, Crane M (2010) Cross-platform microarray data normalisation for regulatory network inference. PLoS ONE 5(11): e13822.
-
(2010)
PLoS ONE
, vol.5
, Issue.11
-
-
Sîrbu, A.1
Ruskin, H.J.2
Crane, M.3
-
137
-
-
84870387877
-
Stages of gene regulatory network inference: the evolutionary algorithm role
-
In: Kita PE (ed), InTech
-
Sîrbu A, Ruskin HJ, Crane M (2011) Stages of gene regulatory network inference: the evolutionary algorithm role. In: Kita PE (ed) Evolutionary algorithms. InTech.
-
(2011)
Evolutionary algorithms
-
-
Sîrbu, A.1
Ruskin, H.J.2
Crane, M.3
-
139
-
-
79960295612
-
-
1st edn., chap. All aboard: toward a machine-friendly scholarly communication system. Microscoft Research
-
de Sompel HV, Lagoze C (2009) The fourth paradigm: data-intensive scientific discovery, 1st edn., chap. All aboard: toward a machine-friendly scholarly communication system. Microscoft Research, pp 193-199.
-
(2009)
The fourth paradigm: data-intensive scientific discovery
, pp. 193-199
-
-
de Sompel, H.V.1
Lagoze, C.2
-
140
-
-
35048877156
-
Optimizing topology and parameters of gene regulatory network models from time-series experiments
-
In: Deb K (eds), Springer, Berlin
-
Spieth C, Streichert F, Speer N, Zell A (2004) Optimizing topology and parameters of gene regulatory network models from time-series experiments. In: Deb K (eds) Genetic and evolutionary computation GECCO 2004. Lecture Notes in computer science, vol 3102. Springer, Berlin, pp 461-470.
-
(2004)
Genetic and evolutionary computation GECCO 2004. Lecture Notes in computer science
, vol.3102
, pp. 461-470
-
-
Spieth, C.1
Streichert, F.2
Speer, N.3
Zell, A.4
-
141
-
-
84894320869
-
Algorithms for modeling gene regulatory networks
-
Spieth C, Streichert F, Supper J, Speer N, Zell A (2005) Algorithms for modeling gene regulatory networks. In: Proceedings of the 2005 IEEE symposium on computational intelligence in bioinformatics and computational biology, 2005. CIBCB '05, pp 1-7.
-
(2005)
Proceedings of the 2005 IEEE symposium on computational intelligence in bioinformatics and computational biology, 2005. CIBCB '05
, pp. 1-7
-
-
Spieth, C.1
Streichert, F.2
Supper, J.3
Speer, N.4
Zell, A.5
-
142
-
-
0000852513
-
Multiobjective optimization using nondominated sorting in genetic algorithms
-
Srinivas N, Deb K (1994) Multiobjective optimization using nondominated sorting in genetic algorithms. Evol Comput 2: 221-248.
-
(1994)
Evolutionary Computation
, vol.2
, pp. 221-248
-
-
Srinivas, N.1
Deb, K.2
-
143
-
-
57049159362
-
A fast, robust and tunable synthetic gene oscillator
-
Stricker J, Cookson S, Bennett MR, Mather WH, Tsimring LS, Hasty J (2008) A fast, robust and tunable synthetic gene oscillator. Nature 456: 516-519.
-
(2008)
Nature
, vol.456
, pp. 516-519
-
-
Stricker, J.1
Cookson, S.2
Bennett, M.R.3
Mather, W.H.4
Tsimring, L.S.5
Hasty, J.6
-
144
-
-
33845479864
-
Modeling gene-regulatory networks using evolutionary algorithms and distributed computing
-
Swain M, Hunniford T, Mandel J, Palfreyman N, Dubitzky W (2005) Modeling gene-regulatory networks using evolutionary algorithms and distributed computing. In: IEEE international symposium on cluster computing and the grid, 2005. CCGrid 2005, vol 1. pp 512-519.
-
(2005)
IEEE international symposium on cluster computing and the grid, 2005. CCGrid 2005
, vol.1
, pp. 512-519
-
-
Swain, M.1
Hunniford, T.2
Mandel, J.3
Palfreyman, N.4
Dubitzky, W.5
-
145
-
-
55749098451
-
Benchmark functions for the CEC 2008 special session and competition on large scale global optimization
-
Nature Inspired Computation and Applications Laboratory (NICAL), China
-
Tang K, Yao X, Suganthan PN, MacNish C, Chen YP, Chen CM, Yang Z (2007) Benchmark functions for the CEC 2008 special session and competition on large scale global optimization. Technical report. Nature Inspired Computation and Applications Laboratory (NICAL), China.
-
(2007)
Technical report
-
-
Tang, K.1
Yao, X.2
Suganthan, P.N.3
MacNish, C.4
Chen, Y.P.5
Chen, C.M.6
Yang, Z.7
-
146
-
-
0037687416
-
Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling
-
Tegnèr J, Yeung MKS, Hasty J, Collins JJ (2003) Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling. Proc Nat Acad Sci 100(10): 5944-5949.
-
(2003)
Proc Nat Acad Sci
, vol.100
, Issue.10
, pp. 5944-5949
-
-
Tegnèr, J.1
Yeung, M.K.S.2
Hasty, J.3
Collins, J.J.4
-
148
-
-
84879676784
-
Evolving connectivity between genetic oscillators and switches using evolutionary algorithms
-
1341001
-
Thomas SA, Jin Y (2013) Evolving connectivity between genetic oscillators and switches using evolutionary algorithms. J Bioinform Comput Biol 11(3): 1341001.
-
(2013)
J Bioinform Comput Biol
, vol.11
, Issue.3
-
-
Thomas, S.A.1
Jin, Y.2
-
149
-
-
84875553363
-
Single and multi-objective in silico evolution of tunable genetic oscillators
-
In: Purshouse R, Fleming P, Fonseca C, Greco S, Shaw J (eds), Springer, Berlin
-
Thomas SA, Jin Y (2013) Single and multi-objective in silico evolution of tunable genetic oscillators. In: Purshouse R, Fleming P, Fonseca C, Greco S, Shaw J (eds) Evolutionary multi-criterion optimization. Lecture Notes in computer science, vol 7811. Springer, Berlin, pp 696-709.
-
(2013)
Evolutionary multi-criterion optimization. Lecture Notes in computer science
, vol.7811
, pp. 696-709
-
-
Thomas, S.A.1
Jin, Y.2
-
151
-
-
4344703653
-
Nonlinear numerical optimization technique based on a genetic algorithm for inverse problems: towards the inference of genetic networks
-
Tominaga D, Okamoto M, Maki Y, Watanabe S, Eguchi Y (1999) Nonlinear numerical optimization technique based on a genetic algorithm for inverse problems: towards the inference of genetic networks. In: German conference on bioinformatics' 99, pp 127-140.
-
(1999)
German conference on bioinformatics' 99
, pp. 127-140
-
-
Tominaga, D.1
Okamoto, M.2
Maki, Y.3
Watanabe, S.4
Eguchi, Y.5
-
152
-
-
84455173311
-
Gene regulatory network reconstruction using bayesian networks, the dantzig selector, the lasso and their meta-analysis
-
e29,165
-
Vignes M, Vandel J, Allouche D, Ramadan-Alban N, Cierco-Ayrolles C, Schiex T, Mangin B, de Givry S (2011) Gene regulatory network reconstruction using bayesian networks, the dantzig selector, the lasso and their meta-analysis. PLoS ONE 6(12): e29165.
-
(2011)
PLoS ONE
, vol.6
, Issue.12
-
-
Vignes, M.1
Vandel, J.2
Allouche, D.3
Ramadan-Alban, N.4
Cierco-Ayrolles, C.5
Schiex, T.6
Mangin, B.7
de Givry, S.8
-
153
-
-
84874386593
-
Model identification: a key challenge is computational systems biology
-
World Publishing Corporation
-
Voit EO (2008) Model identification: a key challenge is computational systems biology. In: Optimization and systems biology. Lecture notes in operations research, vol 9, World Publishing Corporation, pp 1-12. http://www. aporc. org/LNOR/9/OSB2008F01. pdf.
-
(2008)
Optimization and systems biology. Lecture notes in operations research
, vol.9
, pp. 1-12
-
-
Voit, E.O.1
-
154
-
-
4444351989
-
Decoupling dynamical systems for pathway identification from metabolic profiles
-
Voit EO, Almeida J (2004) Decoupling dynamical systems for pathway identification from metabolic profiles. Bioinformatics 20(11): 1670-1681.
-
(2004)
Bioinformatics
, vol.20
, Issue.11
, pp. 1670-1681
-
-
Voit, E.O.1
Almeida, J.2
-
155
-
-
79952109162
-
Optimization meets systems biology
-
Wang Y, Zhang XS, Chen L (2010) Optimization meets systems biology. BMC Syst Biol 4(Suppl 2): 1-4.
-
(2010)
BMC Syst Biol
, vol.4
, Issue.SUPPL. 2
, pp. 1-4
-
-
Wang, Y.1
Zhang, X.S.2
Chen, L.3
-
157
-
-
33746146379
-
The constitution and structure of the lunar interior
-
Wieczorek MA, Jolliff BL, Khan A, Pritchard ME, Weiss BP, Williams JG, Hood LL, Righter K, Neal CR, Shearer CK, McCallum IS, Tompkins S, Hawke BR, Peterson C, Gillis JJ, Bussey B (2006) The constitution and structure of the lunar interior. Rev Mineral Geochem 60: 221-364.
-
(2006)
Reviews in Mineralogy & Geochemistry
, vol.60
, pp. 221-364
-
-
Wieczorek, M.A.1
Jolliff, B.L.2
Khan, A.3
Pritchard, M.E.4
Weiss, B.P.5
Williams, J.G.6
Hood, L.L.7
Righter, K.8
Neal, C.R.9
Shearer, C.K.10
McCallum, I.S.11
Tompkins, S.12
Hawke, B.R.13
Peterson, C.14
Gillis, J.J.15
Bussey, B.16
-
159
-
-
84894379474
-
A parallel algorithm of constructing gene regulatory networks
-
In: Du DZ, Zhang XS (eds), World Publishing Corporation
-
Xiao M, Zhang L, He B, Xie J, Zhang W (2009) A parallel algorithm of constructing gene regulatory networks. In: Du DZ, Zhang XS (eds) Optimization and systems biology. Lecture Notes in operations research, vol 11. World Publishing Corporation, pp 184-188.
-
(2009)
Optimization and systems biology. Lecture Notes in operations research
, vol.11
, pp. 184-188
-
-
Xiao, M.1
Zhang, L.2
He, B.3
Xie, J.4
Zhang, W.5
-
160
-
-
84866642239
-
Gene regulatory network inference from multifactorial perturbation data using both regression and correlation analyses
-
e43,819
-
Xiong J, Zhou T (2012) Gene regulatory network inference from multifactorial perturbation data using both regression and correlation analyses. PLoS ONE 7(9): e43819.
-
(2012)
PLoS ONE
, vol.7
, Issue.9
-
-
Xiong, J.1
Zhou, T.2
-
161
-
-
55749099311
-
Multilevel cooperative coevolution for large scale optimization
-
(IEEE World Congress on Computational Intelligence)
-
Yang Z, Tang K, Yao X (2008) Multilevel cooperative coevolution for large scale optimization. In: IEEE congress on evolutionary computation, 2008. CEC 2008. (IEEE World Congress on Computational Intelligence), pp 1663-1670.
-
(2008)
IEEE congress on evolutionary computation, 2008. CEC 2008
, pp. 1663-1670
-
-
Yang, Z.1
Tang, K.2
Yao, X.3
-
162
-
-
63649099828
-
Gene regulatory network modeling using bayesian networks and cross correlation
-
CIBEC 2008. Cairo International
-
Yavari F, Towhidkhah F, Gharibzadeh S (2008) Gene regulatory network modeling using bayesian networks and cross correlation. In: Biomedical engineering conference, 2008. CIBEC 2008. Cairo International, pp 1-4.
-
(2008)
Biomedical engineering conference, 2008
, pp. 1-4
-
-
Yavari, F.1
Towhidkhah, F.2
Gharibzadeh, S.3
-
163
-
-
77749264188
-
Improved reconstruction of!'italic?'in silico!'/italic?' gene regulatory networks by integrating knockout and perturbation data
-
Yip KY, Alexander RP, Yan KK, Gerstein M (2010) Improved reconstruction of!'italic? 'in silico!'/italic?' gene regulatory networks by integrating knockout and perturbation data. PLoS ONE 5(1): e8121.
-
(2010)
PLoS ONE
, vol.5
, Issue.1
-
-
Yip, K.Y.1
Alexander, R.P.2
Yan, K.K.3
Gerstein, M.4
-
164
-
-
12344259602
-
Advances to bayesian network inference for generating causal networks from observational biological data
-
Yu J, Smith VA, Wang PP, Hartemink AJ, Jarvis ED (2004) Advances to bayesian network inference for generating causal networks from observational biological data. Bioinformatics 20(18): 3594-3603.
-
(2004)
Bioinformatics
, vol.20
, Issue.18
, pp. 3594-3603
-
-
Yu, J.1
Smith, V.A.2
Wang, P.P.3
Hartemink, A.J.4
Jarvis, E.D.5
-
165
-
-
79956210094
-
Robust dynamical network structure reconstruction
-
Yuan Y, Stan GB, Warnick S, Goncalves JM (2011) Robust dynamical network structure reconstruction. Autom Spe Issue Syst Biol 47: 1230-1235.
-
(2011)
Automatica, Special Issue on Systems Biology
, vol.47
, pp. 1230-1235
-
-
Yuan, Y.1
Stan, G.B.2
Warnick, S.3
Goncalves, J.M.4
-
166
-
-
84855160951
-
Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information
-
Zhang X, Zhao XM, He K, Lu L, Cao Y, Liu J, Hao JK, Liu ZP, Chen L (2012) Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information. Bioinformatics 28(1): 98-104.
-
(2012)
Bioinformatics
, vol.28
, Issue.1
, pp. 98-104
-
-
Zhang, X.1
Zhao, X.M.2
He, K.3
Lu, L.4
Cao, Y.5
Liu, J.6
Hao, J.K.7
Liu, Z.P.8
Chen, L.9
-
167
-
-
84871812701
-
Data integration in bioinformatics: current efforts and challenges
-
In: Mahdavi DMA (ed)
-
Zhang Z, Bajic VB, Yu J, Cheung KH, Townsend JP (2011) Data integration in bioinformatics: current efforts and challenges. In: Mahdavi DMA (ed) Trends and methodologies, chap. 2. InTech, pp 41-56.
-
(2011)
Trends and methodologies, chap. 2. InTech
, pp. 41-56
-
-
Zhang, Z.1
Bajic, V.B.2
Yu, J.3
Cheung, K.H.4
Townsend, J.P.5
-
168
-
-
55749113325
-
Dynamic multi-swarm particle swarm optimizer with local search for large scale global optimization
-
CEC 2008. (IEEE World Congress on Computational Intelligence)
-
Zhao SZ, Liang JJ, Suganthan P, Tasgetiren M (2008) Dynamic multi-swarm particle swarm optimizer with local search for large scale global optimization. In: IEEE congress on evolutionary computation, 2008. CEC 2008. (IEEE World Congress on Computational Intelligence), pp 3845-3852.
-
(2008)
IEEE congress on evolutionary computation, 2008
, pp. 3845-3852
-
-
Zhao, S.Z.1
Liang, J.J.2
Suganthan, P.3
Tasgetiren, M.4
-
169
-
-
84870578537
-
Reconstructing dynamic gene regulatory networks from sample-based transcriptional data
-
Zhu H, Rao RSP, Zeng T, Chen L (2012) Reconstructing dynamic gene regulatory networks from sample-based transcriptional data. Nucleic Acids Res 40(21): 10657-10667.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.21
, pp. 10657-10667
-
-
Zhu, H.1
Rao, R.S.P.2
Zeng, T.3
Chen, L.4
|