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Items: 1 to 20 of 169

1.

Inferring biochemical reaction pathways: the case of the gemcitabine pharmacokinetics.

Lecca P, Morpurgo D, Fantaccini G, Casagrande A, Priami C.

BMC Syst Biol. 2012 May 28;6:51. doi: 10.1186/1752-0509-6-51.

2.

An integrative network inference approach to predict mechanisms of cancer chemoresistance.

Lecca P.

Integr Biol (Camb). 2013 Mar;5(3):458-73. doi: 10.1039/c2ib20205k.

PMID:
23340828
3.

Biological network inference for drug discovery.

Lecca P, Priami C.

Drug Discov Today. 2013 Mar;18(5-6):256-64. doi: 10.1016/j.drudis.2012.11.001. Epub 2012 Nov 10. Review.

PMID:
23147668
4.

Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent.

Wang Y, Christley S, Mjolsness E, Xie X.

BMC Syst Biol. 2010 Jul 21;4:99. doi: 10.1186/1752-0509-4-99.

5.

Sets2Networks: network inference from repeated observations of sets.

Clark NR, Dannenfelser R, Tan CM, Komosinski ME, Ma'ayan A.

BMC Syst Biol. 2012 Jul 23;6:89. doi: 10.1186/1752-0509-6-89.

6.

Identification of regulatory structure and kinetic parameters of biochemical networks via mixed-integer dynamic optimization.

Guillén-Gosálbez G, Miró A, Alves R, Sorribas A, Jiménez L.

BMC Syst Biol. 2013 Oct 31;7:113. doi: 10.1186/1752-0509-7-113.

7.

Identification of a metabolic reaction network from time-series data of metabolite concentrations.

Sriyudthsak K, Shiraishi F, Hirai MY.

PLoS One. 2013;8(1):e51212. doi: 10.1371/journal.pone.0051212. Epub 2013 Jan 10.

8.

Genetic network inference as a series of discrimination tasks.

Kimura S, Nakayama S, Hatakeyama M.

Bioinformatics. 2009 Apr 1;25(7):918-25. doi: 10.1093/bioinformatics/btp072. Epub 2009 Feb 2.

9.

New Markov-Shannon Entropy models to assess connectivity quality in complex networks: from molecular to cellular pathway, Parasite-Host, Neural, Industry, and Legal-Social networks.

Riera-Fernández P, Munteanu CR, Escobar M, Prado-Prado F, Martín-Romalde R, Pereira D, Villalba K, Duardo-Sánchez A, González-Díaz H.

J Theor Biol. 2012 Jan 21;293:174-88. doi: 10.1016/j.jtbi.2011.10.016. Epub 2011 Oct 25.

PMID:
22037044
10.

An approach for dynamical network reconstruction of simple network motifs.

Nakatsui M, Araki M, Kondo A.

BMC Syst Biol. 2013;7 Suppl 6:S4. doi: 10.1186/1752-0509-7-S6-S4. Epub 2013 Dec 13.

11.

Inferring differences in the distribution of reaction rates across conditions.

Hendrickx DM, Hoefsloot HC, Hendriks MM, Vis DJ, Canelas AB, Teusink B, Smilde AK.

Mol Biosyst. 2012 Sep;8(9):2415-23. Epub 2012 Jul 11.

PMID:
22782002
12.

Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems.

Jenkinson G, Zhong X, Goutsias J.

BMC Bioinformatics. 2010 Nov 5;11:547. doi: 10.1186/1471-2105-11-547.

13.

Calibration of dynamic models of biological systems with KInfer.

Lecca P, Palmisano A, Ihekwaba A, Priami C.

Eur Biophys J. 2010 May;39(6):1019-39. doi: 10.1007/s00249-009-0520-3. Epub 2009 Aug 11.

PMID:
19669750
14.

Stability of metabolic correlations under changing environmental conditions in Escherichia coli--a systems approach.

Szymanski J, Jozefczuk S, Nikoloski Z, Selbig J, Nikiforova V, Catchpole G, Willmitzer L.

PLoS One. 2009 Oct 15;4(10):e7441. doi: 10.1371/journal.pone.0007441.

15.

Computational approaches to the topology, stability and dynamics of metabolic networks.

Steuer R.

Phytochemistry. 2007 Aug-Sep;68(16-18):2139-51. Epub 2007 Jun 14.

PMID:
17574639
16.

Identification of biochemical networks by S-tree based genetic programming.

Cho DY, Cho KH, Zhang BT.

Bioinformatics. 2006 Jul 1;22(13):1631-40. Epub 2006 Apr 3.

17.

Gene expression complex networks: synthesis, identification, and analysis.

Lopes FM, Cesar RM, Costa Lda F.

J Comput Biol. 2011 Oct;18(10):1353-67. doi: 10.1089/cmb.2010.0118. Epub 2011 May 6.

PMID:
21548810
18.

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. doi: 10.1016/j.ygeno.2009.01.006. Epub 2009 Feb 5.

19.

Identification of metabolic system parameters using global optimization methods.

Polisetty PK, Voit EO, Gatzke EP.

Theor Biol Med Model. 2006 Jan 27;3:4.

20.

An intelligent two-stage evolutionary algorithm for dynamic pathway identification from gene expression profiles.

Ho SY, Hsieh CH, Yu FC, Huang HL.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Oct-Dec;4(4):648-60.

PMID:
17975275
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