Irene Cantone 1, Lucia Marucci 1, 2, Francesco Iorio 1, Maria Aurelia Ricci 1, Vincenzo Belcastro 1, Mukesh Bansal 1, Stefania Santini 2, Mario di Bernardo 2, Diego di Bernardo 1, 2, 3, @, and Maria Pia Cosma 1, 3, @,
1 Telethon Institute of Genetics and Medicine (TIGEM),
Naples 80131, Italy
2 Department of Computer and Systems Engineering, University
of Naples Federico II, Naples 80125, Italy
3 These authors contributed equally to this work
Correspondence: dibernardo@tigem.it
(D.d.B), cosma@tigem.it (M.P.C.)
Summary
Related Articles from PubMed
Further Information
Systems biology approaches are extensively used to model and reverse engineer gene regulatory networks from experimental data. Conversely, synthetic biology allows de novo construction of a regulatory network to seed new functions in the cell. At present, the usefulness and predictive ability of modeling and reverse engineering cannot be assessed and compared rigorously. We built in the yeast Saccharomyces cerevisiae a synthetic network, IRMA, for in vivo benchmarking of reverse-engineering and modeling approaches. The network is composed of five genes regulating each other through a variety of regulatory interactions; it is negligibly affected by endogenous genes, and it is responsive to small molecules. We measured time series and steady-state expression data after multiple perturbations. These data were used to assess state-of-the-art modeling and reverse-engineering techniques. A semiquantitative model was able to capture and predict the behavior of the network. Reverse engineering based on differential equations and Bayesian networks correctly inferred regulatory interactions from the experimental data.
1: Reverse engineering and verification of gene networks: Principles, assumptions, and limitations of present methods and future perspectives.
He F, Balling R, Zeng AP.
J Biotechnol. 2009 Jul 22. [Epub ahead of print]
PMID: 19631244 [PubMed - as supplied by publisher]
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2: Developmental Engineering: A new paradigm for the design and manufacturing of cell based products Part II. From genes to networks: tissue engineering from the viewpoint of systems biology and network science.
Lenas P, Moos MJ, Luyten F.
Tissue Eng Part B Rev. 2009 Jul 9. [Epub ahead of print]
PMID: 19589040 [PubMed - as supplied by publisher]
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3: Reconstruct gene regulatory network using slice pattern model.
Wang Y, Wang G, Yang B, Tao H, Yang JY, Deng Y, Liu Y.
BMC Genomics. 2009 Jul 7;10 Suppl 1:S2.
PMID: 19594879 [PubMed - indexed for MEDLINE]
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4: Reverse engineering module networks by PSO-RNN hybrid modeling.
Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW.
BMC Genomics. 2009 Jul 7;10 Suppl 1:S15.
PMID: 19594874 [PubMed - indexed for MEDLINE]
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5: List-decoding methods for inferring polynomials in finite dynamical gene network models.
Dingel J, Milenkovic O.
Bioinformatics. 2009 Jul 1;25(13):1686-93. Epub 2009 Apr 28.
PMID: 19401400 [PubMed - in process]
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6: Predictive modeling in cancer: where systems biology meets the stock market.
Abbod MF, Hamdy FC, Linkens DA, Catto JW.
Expert Rev Anticancer Ther. 2009 Jul;9(7):867-70. No abstract available.
PMID: 19589024 [PubMed - in process]
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7:Towards the automated engineering of a synthetic genome.
Carrera J, Rodrigo G, Jaramillo A.
Mol Biosyst. 2009 Jul;5(7):733-43. Epub 2009 May 28.
PMID: 19562112 [PubMed - in process]
Related Articles
8: Synthetic biology: exploring and exploiting genetic modularity through the design of novel biological networks.
Agapakis CM, Silver PA.
Mol Biosyst. 2009 Jul;5(7):704-13. Epub 2009 May 14.
PMID: 19562109 [PubMed - in process]
Related Articles
9: A systematic design method for robust synthetic biology to satisfy design specifications.
Chen BS, Wu CH.
BMC Syst Biol. 2009 Jun 30;3(1):66. [Epub ahead of print]
PMID: 19566953 [PubMed - as supplied by publisher]
Related Articles Free article at journal site
10: Modeling stochasticity and robustness in gene regulatory networks.
Garg A, Mohanram K, Di Cara A, De Micheli G, Xenarios I.
Bioinformatics. 2009 Jun 15;25(12):i101-9.
PMID: 19477975 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
11:
Dynamical approaches to modeling developmental gene regulatory networks.
Geard N, Willadsen K.
Birth Defects Res C Embryo Today. 2009 Jun;87(2):131-42.
PMID: 19530129 [PubMed - in process]
Related Articles
12:
Systems and Synthetic biology: tackling genetic networks and complex diseases.
Cuccato G, Della Gatta G, di Bernardo D.
Heredity. 2009 Jun;102(6):527-32. Epub 2009 Mar 4. Review.
PMID: 19259117 [PubMed - indexed for MEDLINE]
Related Articles
13:
Synthetic gene networks: the next wave in biotechnology?
Bhalerao KD.
Trends Biotechnol. 2009 Jun;27(6):368-74. Epub 2009 May 4. Review.
PMID: 19409633 [PubMed - indexed for MEDLINE]
Related Articles
14:
Designing switchable enzymes.
Ostermeier M.
Curr Opin Struct Biol. 2009 May 25. [Epub ahead of print]
PMID: 19473830 [PubMed - as supplied by publisher]
Related Articles
15:
The effect of network topology on the stability of discrete state models of genetic control.
Pomerance A, Ott E, Girvan M, Losert W.
Proc Natl Acad Sci U S A. 2009 May 19;106(20):8209-14. Epub 2009 Apr 29.
PMID: 19416903 [PubMed - indexed for MEDLINE]
Related Articles
16:
Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks.
Michoel T, De Smet R, Joshi A, Van de Peer Y, Marchal K.
BMC Syst Biol. 2009 May 7;3:49.
PMID: 19422680 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
17:
Model selection in the reconstruction of regulatory networks from time-series data.
Novikov E, Barillot E.
BMC Res Notes. 2009 May 5;2:68.
PMID: 19416509 [PubMed - in process]
Related Articles Free article in PMC | at journal site
18:
GeNGe: systematic generation of gene regulatory networks.
Hache H, Wierling C, Lehrach H, Herwig R.
Bioinformatics. 2009 May 1;25(9):1205-7. Epub 2009 Feb 27.
PMID: 19251773 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
19:
Inference of active transcriptional networks by integration of gene expression kinetics modeling and multisource data.
Vu TT, Vohradsky J.
Genomics. 2009 May;93(5):426-33. Epub 2009 Feb 5.
PMID: 19442636 [PubMed - indexed for MEDLINE]
Related Articles
20:
Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast.
Song M, Ouyang Z, Liu ZL.
IET Syst Biol. 2009 May;3(3):203-18.
PMID: 19449980 [PubMed - indexed for MEDLINE]
Related Articles
21:
Genetic network identification using convex programming.
Julius A, Zavlanos M, Boyd S, Pappas GJ.
IET Syst Biol. 2009 May;3(3):155-66.
PMID: 19449976 [PubMed - indexed for MEDLINE]
Related Articles
22:
Diversity-based, model-guided construction of synthetic gene networks with predicted functions.
Ellis T, Wang X, Collins JJ.
Nat Biotechnol. 2009 May;27(5):465-71. Epub 2009 Apr 19.
PMID: 19377462 [PubMed - indexed for MEDLINE]
Related Articles
23:
Systems biology strikes gold.
Camacho DM, Collins JJ.
Cell. 2009 Apr 3;137(1):24-6.
PMID: 19345182 [PubMed - indexed for MEDLINE]
Related Articles
24:
A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches.
Cantone I, Marucci L, Iorio F, Ricci MA, Belcastro V, Bansal M, Santini S, di Bernardo M, di Bernardo D, Cosma MP.
Cell. 2009 Apr 3;137(1):172-81. Epub 2009 Mar 26.
PMID: 19327819 [PubMed - indexed for MEDLINE]
Related Articles
25:
Model-based redesign of global transcription regulation.
Carrera J, Rodrigo G, Jaramillo A.
Nucleic Acids Res. 2009 Apr;37(5):e38. Epub 2009 Feb 2.
PMID: 19188257 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
26:
Engineering of synthetic mammalian gene networks.
Weber W, Fussenegger M.
Chem Biol. 2009 Mar 27;16(3):287-97. Review.
PMID: 19318210 [PubMed - indexed for MEDLINE]
Related Articles
27:
Network benchmarking: a happy marriage between systems and synthetic biology.
Minty JJ, Varedi K SM, Nina Lin X.
Chem Biol. 2009 Mar 27;16(3):239-41.
PMID: 19318204 [PubMed - indexed for MEDLINE]
Related Articles
28:
Information processing in the transcriptional regulatory network of yeast: functional robustness.
Emmert-Streib F, Dehmer M.
BMC Syst Biol. 2009 Mar 19;3:35.
PMID: 19298671 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
29:
Benchmarking regulatory network reconstruction with GRENDEL.
Haynes BC, Brent MR.
Bioinformatics. 2009 Mar 15;25(6):801-7. Epub 2009 Feb 2.
PMID: 19188190 [PubMed - indexed for MEDLINE]
Related Articles
30:
Inferring gene networks: dream or nightmare?
Scheinine A, Mentzen WI, Fotia G, Pieroni E, Maggio F, Mancosu G, de la Fuente A.
Ann N Y Acad Sci. 2009 Mar;1158:287-301.
PMID: 19348650 [PubMed - indexed for MEDLINE]
Related Articles
31:
Reverse engineering of gene networks with LASSO and nonlinear basis functions.
Gustafsson M, Hörnquist M, Lundström J, Björkegren J, Tegnér J.
Ann N Y Acad Sci. 2009 Mar;1158:265-75.
PMID: 19348648 [PubMed - indexed for MEDLINE]
Related Articles
32:
NIRest: a tool for gene network and mode of action inference.
Lauria M, Iorio F, di Bernardo D.
Ann N Y Acad Sci. 2009 Mar;1158:257-64.
PMID: 19348647 [PubMed - indexed for MEDLINE]
Related Articles
33:
Replaying the evolutionary tape: biomimetic reverse engineering of gene networks.
Marbach D, Mattiussi C, Floreano D.
Ann N Y Acad Sci. 2009 Mar;1158:234-45.
PMID: 19348645 [PubMed - indexed for MEDLINE]
Related Articles
34:
A gene network simulator to assess reverse engineering algorithms.
Di Camillo B, Toffolo G, Cobelli C.
Ann N Y Acad Sci. 2009 Mar;1158:125-42.
PMID: 19348638 [PubMed - indexed for MEDLINE]
Related Articles
35:
Network inference by combining biologically motivated regulatory constraints with penalized regression.
Parisi F, Koeppl H, Naef F.
Ann N Y Acad Sci. 2009 Mar;1158:114-24.
PMID: 19348637 [PubMed - indexed for MEDLINE]
Related Articles
36:
Combining multiple results of a reverse-engineering algorithm: application to the DREAM five-gene network challenge.
Marbach D, Mattiussi C, Floreano D.
Ann N Y Acad Sci. 2009 Mar;1158:102-13.
PMID: 19348636 [PubMed - indexed for MEDLINE]
Related Articles
37:
Modeling of gene regulatory network dynamics using threshold logic.
Gowda T, Vrudhula S, Kim S.
Ann N Y Acad Sci. 2009 Mar;1158:71-81.
PMID: 19348633 [PubMed - indexed for MEDLINE]
Related Articles
38:
Reverse-engineering transcriptional modules from gene expression data.
Michoel T, De Smet R, Joshi A, Marchal K, Van de Peer Y.
Ann N Y Acad Sci. 2009 Mar;1158:36-43.
PMID: 19348630 [PubMed - indexed for MEDLINE]
Related Articles
39:
Analysis of gene sets based on the underlying regulatory network.
Shojaie A, Michailidis G.
J Comput Biol. 2009 Mar;16(3):407-26.
PMID: 19254181 [PubMed - indexed for MEDLINE]
Related Articles
40:
Generating realistic in silico gene networks for performance assessment of reverse engineering methods.
Marbach D, Schaffter T, Mattiussi C, Floreano D.
J Comput Biol. 2009 Feb;16(2):229-39.
PMID: 19183003 [PubMed - indexed for MEDLINE]
Related Articles
41:
A network biology approach to aging in yeast.
Lorenz DR, Cantor CR, Collins JJ.
Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):1145-50. Epub 2009 Jan 21.
PMID: 19164565 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
42:
Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae.
Christensen TS, Oliveira AP, Nielsen J.
BMC Syst Biol. 2009 Jan 14;3:7.
PMID: 19144179 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
43:
Single-Cell Microscopy, Systems Biology, and Modeling Approaches in Cell Biology.
van Oudenaarden A, Muzzey D.
Annu Rev Cell Dev Biol. 2009 Jan 12. [Epub ahead of print] No abstract available.
PMID: 19575655 [PubMed - as supplied by publisher]
Related Articles
44:
Predicting genetic interactions with random walks on biological networks.
Chipman KC, Singh AK.
BMC Bioinformatics. 2009 Jan 12;10:17.
PMID: 19138426 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
45:
Reverse Engineering of Gene Regulatory Networks: A Comparative Study.
Hache H, Lehrach H, Herwig R.
EURASIP J Bioinform Syst Biol. 2009;2009:617281. Epub 2009 Jun 11.
PMID: 19551137 [PubMed - as supplied by publisher]
Related Articles Free article in PMC | at journal site
46:
Engineering prokaryotic gene circuits.
Michalodimitrakis K, Isalan M.
FEMS Microbiol Rev. 2009 Jan;33(1):27-37. Epub 2008 Nov 4. Review.
PMID: 19016883 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
47:
Systems biology of microbial communities.
Navid A, Ghim CM, Fenley AT, Yoon S, Lee S, Almaas E.
Methods Mol Biol. 2009;500:469-94.
PMID: 19399434 [PubMed - indexed for MEDLINE]
Related Articles
48:
Methods for the inference of biological pathways and networks.
Bumgarner RE, Yeung KY.
Methods Mol Biol. 2009;541:225-45. Review.
PMID: 19381545 [PubMed - indexed for MEDLINE]
Related Articles
49:
Effects of functional bias on supervised learning of a gene network model.
Lee I, Marcotte EM.
Methods Mol Biol. 2009;541:463-75. Review.
PMID: 19381535 [PubMed - indexed for MEDLINE]
Related Articles
50:
The transition from differential equations to Boolean networks: a case study in simplifying a regulatory network model.
Davidich M, Bornholdt S.
J Theor Biol. 2008 Dec 7;255(3):269-77. Epub 2008 Jul 23.
PMID: 18692073 [PubMed - indexed for MEDLINE]
Related Articles
51:
Microbial systems biology: new frontiers open to predictive microbiology.
Brul S, Mensonides FI, Hellingwerf KJ, Teixeira de Mattos MJ.
Int J Food Microbiol. 2008 Nov 30;128(1):16-21. Epub 2008 May 6. Review.
PMID: 18541320 [PubMed - indexed for MEDLINE]
Related Articles
52:
Stochastic analysis of the GAL genetic switch in Saccharomyces cerevisiae: modeling and experiments reveal hierarchy in glucose repression.
Prasad V, Venkatesh KV.
BMC Syst Biol. 2008 Nov 17;2:97.
PMID: 19014615 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
53:
Epistasis--the essential role of gene interactions in the structure and evolution of genetic systems.
Phillips PC.
Nat Rev Genet. 2008 Nov;9(11):855-67. Review.
PMID: 18852697 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
54:
A predictive model of the oxygen and heme regulatory network in yeast.
Kundaje A, Xin X, Lan C, Lianoglou S, Zhou M, Zhang L, Leslie C.
PLoS Comput Biol. 2008 Nov;4(11):e1000224. Epub 2008 Nov 14.
PMID: 19008939 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
55:
Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes.
Dixon SJ, Fedyshyn Y, Koh JL, Prasad TS, Chahwan C, Chua G, Toufighi K, Baryshnikova A, Hayles J, Hoe KL, Kim DU, Park HO, Myers CL, Pandey A, Durocher D, Andrews BJ, Boone C.
Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16653-8. Epub 2008 Oct 17.
PMID: 18931302 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
56:
Control of transcriptional variability by overlapping feed-forward regulatory motifs.
Ratushny AV, Ramsey SA, Roda O, Wan Y, Smith JJ, Aitchison JD.
Biophys J. 2008 Oct;95(8):3715-23. Epub 2008 Jul 11.
PMID: 18621837 [PubMed - indexed for MEDLINE]
Related Articles
57:
Toward integration of in vivo molecular computing devices: successes and challenges.
Hayat S, Hinze T.
HFSP J. 2008 Oct;2(5):239-43. Epub 2008 Aug 13.
PMID: 19404433 [PubMed - in process]
Related Articles Free article in PMC
58:
Network legos: building blocks of cellular wiring diagrams.
Murali TM, Rivera CG.
J Comput Biol. 2008 Sep;15(7):829-44.
PMID: 18707557 [PubMed - indexed for MEDLINE]
Related Articles
59:
Systems biology: Reverse engineering the cell.
Ingolia NT, Weissman JS.
Nature. 2008 Aug 28;454(7208):1059-62. No abstract available.
PMID: 18756243 [PubMed - indexed for MEDLINE]
Related Articles
60:
Gene regulatory network inference using out of equilibrium statistical mechanics.
Benecke A.
HFSP J. 2008 Aug;2(4):183-8. Epub 2008 Jul 23.
PMID: 19404429 [PubMed - in process]
Related Articles Free article in PMC
61:
Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks.
Zhu J, Zhang B, Smith EN, Drees B, Brem RB, Kruglyak L, Bumgarner RE, Schadt EE.
Nat Genet. 2008 Jul;40(7):854-61. Epub 2008 Jun 15.
PMID: 18552845 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
62:
Applying intelligent computing techniques to modeling biological networks from expression data.
Lee WP, Yang KC.
Genomics Proteomics Bioinformatics. 2008 Jun;6(2):111-20.
PMID: 18973867 [PubMed - indexed for MEDLINE]
Related Articles
63:
A copula method for modeling directional dependence of genes.
Kim JM, Jung YS, Sungur EA, Han KH, Park C, Sohn I.
BMC Bioinformatics. 2008 May 1;9:225.
PMID: 18447957 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
64:
Network-guided genetic screening: building, testing and using gene networks to predict gene function.
Lehner B, Lee I.
Brief Funct Genomic Proteomic. 2008 May;7(3):217-27. Epub 2008 Apr 29. Review.
PMID: 18445637 [PubMed - indexed for MEDLINE]
Related Articles
65:
One hub-one process: a tool based view on regulatory network topology.
Axelsen JB, Bernhardsson S, Sneppen K.
BMC Syst Biol. 2008 Mar 4;2:25.
PMID: 18318890 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
66:
Structural systems identification of genetic regulatory networks.
Xiong H, Choe Y.
Bioinformatics. 2008 Feb 15;24(4):553-60. Epub 2008 Jan 5.
PMID: 18175769 [PubMed - indexed for MEDLINE]
Related Articles Free article at journal site
67:
Comparative analysis of the transcription-factor gene regulatory networks of E. coli and S. cerevisiae.
Guzmán-Vargas L, Santillán M.
BMC Syst Biol. 2008 Jan 31;2:13.
PMID: 18237429 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
68:
Predicting biological system objectives de novo from internal state measurements.
Gianchandani EP, Oberhardt MA, Burgard AP, Maranas CD, Papin JA.
BMC Bioinformatics. 2008 Jan 24;9:43.
PMID: 18218092 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
69:
Function approximation approach to the inference of reduced NGnet models of genetic networks.
Kimura S, Sonoda K, Yamane S, Maeda H, Matsumura K, Hatakeyama M.
BMC Bioinformatics. 2008 Jan 14;9:23.
PMID: 18194576 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
70:
Systems approaches to identifying gene regulatory networks in plants.
Long TA, Brady SM, Benfey PN.
Annu Rev Cell Dev Biol. 2008;24:81-103. Review.
PMID: 18616425 [PubMed - indexed for MEDLINE]
Related Articles
71:
Inferring regulatory networks.
Li H, Xuan J, Wang Y, Zhan M.
Front Biosci. 2008 Jan 1;13:263-75. Review.
PMID: 17981545 [PubMed - indexed for MEDLINE]
Related Articles
72:
Comparison of reverse-engineering methods using an in silico network.
Camacho D, Vera Licona P, Mendes P, Laubenbacher R.
Ann N Y Acad Sci. 2007 Dec;1115:73-89. Epub 2007 Oct 9. Review.
PMID: 17925358 [PubMed - indexed for MEDLINE]
Related Articles
73:
Benchmarking of dynamic Bayesian networks inferred from stochastic time-series data.
David LA, Wiggins CH.
Ann N Y Acad Sci. 2007 Dec;1115:90-101. Epub 2007 Oct 9.
PMID: 17925346 [PubMed - indexed for MEDLINE]
Related Articles
74:
Steady state approach to model gene regulatory networks--simulation of microarray experiments.
Rawool SB, Venkatesh KV.
Biosystems. 2007 Nov-Dec;90(3):636-55. Epub 2007 Feb 17.
PMID: 17382459 [PubMed - indexed for MEDLINE]
Related Articles
75:
Comparison of probabilistic Boolean network and dynamic Bayesian network approaches for inferring gene regulatory networks.
Li P, Zhang C, Perkins EJ, Gong P, Deng Y.
BMC Bioinformatics. 2007 Nov 1;8 Suppl 7:S13.
PMID: 18047712 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
76:
Identifying dynamical modules from genetic regulatory systems: applications to the segment polarity network.
Irons DJ, Monk NA.
BMC Bioinformatics. 2007 Oct 25;8:413.
PMID: 17961242 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
77:
Bridge and brick network motifs: identifying significant building blocks from complex biological systems.
Huang CY, Cheng CY, Sun CT.
Artif Intell Med. 2007 Oct;41(2):117-27. Epub 2007 Sep 7.
PMID: 17825540 [PubMed - indexed for MEDLINE]
Related Articles
78:
A hybrid Bayesian network learning method for constructing gene networks.
Wang M, Chen Z, Cloutier S.
Comput Biol Chem. 2007 Oct;31(5-6):361-72. Epub 2007 Aug 19.
PMID: 17889617 [PubMed - indexed for MEDLINE]
Related Articles
79:
Inference of genetic regulatory networks with recurrent neural network models using particle swarm optimization.
Xu R, Wunsch Ii D, Frank R.
IEEE/ACM Trans Comput Biol Bioinform. 2007 Oct-Dec;4(4):681-92.
PMID: 17975278 [PubMed - indexed for MEDLINE]
Related Articles
80:
Inferring gene regulatory networks using differential evolution with local search heuristics.
Noman N, Iba H.
IEEE/ACM Trans Comput Biol Bioinform. 2007 Oct-Dec;4(4):634-47.
PMID: 17975274 [PubMed - indexed for MEDLINE]
Related Articles
81:
Inferring adaptive regulation thresholds and association rules from gene expression data through combinatorial optimization learning.
Ponzoni I, Azuaje F, Augusto J, Glass D.
IEEE/ACM Trans Comput Biol Bioinform. 2007 Oct-Dec;4(4):624-34.
PMID: 17975273 [PubMed - indexed for MEDLINE]
Related Articles
82:
Underlying principles of natural selection in network evolution: systems biology approach.
Chen BS, Wu WS.
Evol Bioinform Online. 2007 Sep 26;3:245-62.
PMID: 19468310 [PubMed - in process]
Related Articles Free article in PMC
83:
Mining and state-space modeling and verification of sub-networks from large-scale biomolecular networks.
Hu X, Wu FX.
BMC Bioinformatics. 2007 Aug 31;8:324.
PMID: 17764552 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
84:
Modeling gene expression regulatory networks with the sparse vector autoregressive model.
Fujita A, Sato JR, Garay-Malpartida HM, Yamaguchi R, Miyano S, Sogayar MC, Ferreira CE.
BMC Syst Biol. 2007 Aug 30;1:39.
PMID: 17761000 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
85:
Inferring gene regulatory networks from temporal expression profiles under time-delay and noise.
Kim S, Kim J, Cho KH.
Comput Biol Chem. 2007 Aug;31(4):239-45. Epub 2007 Apr 6.
PMID: 17631421 [PubMed - indexed for MEDLINE]
Related Articles
86:
Biological network mapping and source signal deduction.
Brynildsen MP, Wu TY, Jang SS, Liao JC.
Bioinformatics. 2007 Jul 15;23(14):1783-91. Epub 2007 May 11.
PMID: 17495996 [PubMed - indexed for MEDLINE]
Related Articles Free article at journal site
87:
Bayesian Orthogonal Least Squares (BOLS) algorithm for reverse engineering of gene regulatory networks.
Kim CS.
BMC Bioinformatics. 2007 Jul 13;8:251.
PMID: 17626641 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
88:
Indeterminacy of reverse engineering of Gene Regulatory Networks: the curse of gene elasticity.
Krishnan A, Giuliani A, Tomita M.
PLoS One. 2007 Jun 27;2(6):e562.
PMID: 17593963 [PubMed]
Related Articles Free article in PMC | at journal site
89:
An effective data mining technique for reconstructing gene regulatory networks from time series expression data.
Ma PC, Chan KC.
J Bioinform Comput Biol. 2007 Jun;5(3):651-68.
PMID: 17688310 [PubMed - indexed for MEDLINE]
Related Articles
90:
Faithful modeling of transient expression and its application to elucidating negative feedback regulation.
Rubinstein A, Gurevich V, Kasulin-Boneh Z, Pnueli L, Kassir Y, Pinter RY.
Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6241-6. Epub 2007 Mar 30.
PMID: 17400752 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
91:
Plasticity of genetic interactions in metabolic networks of yeast.
Harrison R, Papp B, Pál C, Oliver SG, Delneri D.
Proc Natl Acad Sci U S A. 2007 Feb 13;104(7):2307-12. Epub 2007 Feb 6.
PMID: 17284612 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
92:
Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge.
Geier F, Timmer J, Fleck C.
BMC Syst Biol. 2007 Feb 2;1:11.
PMID: 17408501 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
93:
Bayesian learning of sparse gene regulatory networks.
Chan ZS, Collins L, Kasabov N.
Biosystems. 2007 Feb;87(2-3):299-306. Epub 2006 Sep 10.
PMID: 17223483 [PubMed - indexed for MEDLINE]
Related Articles
94:
In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiae.
Alves R, Sorribas A.
BMC Syst Biol. 2007 Jan 31;1:10.
PMID: 17408500 [PubMed - indexed for MEDLINE]
Related Articles Free article in PMC | at journal site
95:
Identification of functional modules using network topology and high-throughput data.
Ulitsky I, Shamir R.
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114:
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134:
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136:
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137:
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138:
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139:
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141:
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142:
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143:
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144:
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145:
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146:
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147:
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148:
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149:
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150:
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