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Items: 1 to 20 of 96

1.

Towards genome-scale signalling network reconstructions.

Hyduke DR, Palsson BØ.

Nat Rev Genet. 2010 Apr;11(4):297-307. doi: 10.1038/nrg2750. Review.

PMID:
20177425
2.

Simplified models of biological networks.

Sneppen K, Krishna S, Semsey S.

Annu Rev Biophys. 2010;39:43-59. doi: 10.1146/annurev.biophys.093008.131241. Review.

PMID:
20192769
3.

Arabidopsis MAPKs: a complex signalling network involved in multiple biological processes.

Colcombet J, Hirt H.

Biochem J. 2008 Jul 15;413(2):217-26. doi: 10.1042/BJ20080625. Review.

PMID:
18570633
4.

Integrative content-driven concepts for bioinformatics "beyond the cell".

Wingender E, Crass T, Hogan JD, Kel AE, Kel-Margoulis OV, Potapov AP.

J Biosci. 2007 Jan;32(1):169-80. Erratum in: J Biosci. 2007 Jun;32(4):805.

5.

Identification of functional differences in metabolic networks using comparative genomics and constraint-based models.

Hamilton JJ, Reed JL.

PLoS One. 2012;7(4):e34670. doi: 10.1371/journal.pone.0034670. Epub 2012 Apr 16.

6.

A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models.

Ryll A, Bucher J, Bonin A, Bongard S, Gonçalves E, Saez-Rodriguez J, Niklas J, Klamt S.

Biosystems. 2014 Oct;124:26-38. doi: 10.1016/j.biosystems.2014.07.002. Epub 2014 Jul 23.

PMID:
25063553
7.

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis.

Chandrasekaran S, Price ND.

Proc Natl Acad Sci U S A. 2010 Oct 12;107(41):17845-50. doi: 10.1073/pnas.1005139107. Epub 2010 Sep 27.

8.

Reconstruction of microbial transcriptional regulatory networks.

Herrgård MJ, Covert MW, Palsson BØ.

Curr Opin Biotechnol. 2004 Feb;15(1):70-7. Review.

PMID:
15102470
9.

Modular analysis of biological networks.

Kaltenbach HM, Stelling J.

Adv Exp Med Biol. 2012;736:3-17. doi: 10.1007/978-1-4419-7210-1_1. Review.

PMID:
22161320
10.

Information content and scalability in signal transduction network reconstruction formats.

Rother M, Münzner U, Thieme S, Krantz M.

Mol Biosyst. 2013 Aug;9(8):1993-2004. doi: 10.1039/c3mb00005b. Epub 2013 May 2. Review.

PMID:
23636168
11.

Refining metabolic models and accounting for regulatory effects.

Kim J, Reed JL.

Curr Opin Biotechnol. 2014 Oct;29:34-8. doi: 10.1016/j.copbio.2014.02.009. Epub 2014 Mar 14. Review.

PMID:
24632483
12.

A guide to integrating transcriptional regulatory and metabolic networks using PROM (probabilistic regulation of metabolism).

Simeonidis E, Chandrasekaran S, Price ND.

Methods Mol Biol. 2013;985:103-12. doi: 10.1007/978-1-62703-299-5_6.

PMID:
23417801
13.

Network analysis: a new approach to study endocrine disorders.

Stevens A, De Leonibus C, Hanson D, Dowsey AW, Whatmore A, Meyer S, Donn RP, Chatelain P, Banerjee I, Cosgrove KE, Clayton PE, Dunne MJ.

J Mol Endocrinol. 2013 Dec 19;52(1):R79-93. doi: 10.1530/JME-13-0112. Print 2014 Feb. Review.

PMID:
24085748
14.

Building synthetic systems to learn nature's design principles.

Davidson EA, Windram OP, Bayer TS.

Adv Exp Med Biol. 2012;751:411-29. doi: 10.1007/978-1-4614-3567-9_19. Review.

PMID:
22821469
15.

Cancer systems biology: exploring cancer-associated genes on cellular networks.

Wang E, Lenferink A, O'Connor-McCourt M.

Cell Mol Life Sci. 2007 Jul;64(14):1752-62. Review.

PMID:
17415519
16.
17.

Flux balance analysis of biological systems: applications and challenges.

Raman K, Chandra N.

Brief Bioinform. 2009 Jul;10(4):435-49. doi: 10.1093/bib/bbp011. Epub 2009 Mar 15.

PMID:
19287049
18.

DYVIPAC: an integrated analysis and visualisation framework to probe multi-dimensional biological networks.

Nguyen LK, Degasperi A, Cotter P, Kholodenko BN.

Sci Rep. 2015 Jul 29;5:12569. doi: 10.1038/srep12569.

19.

Use of genome-scale metabolic models in evolutionary systems biology.

Papp B, Szappanos B, Notebaart RA.

Methods Mol Biol. 2011;759:483-97. doi: 10.1007/978-1-61779-173-4_27. Review.

PMID:
21863504
20.

Assessment of crosstalks between the Snf1 kinase complex and sphingolipid metabolism in S. cerevisiae via systems biology approaches.

Borklu Yucel E, Ulgen KO.

Mol Biosyst. 2013 Nov;9(11):2914-31. doi: 10.1039/c3mb70248k.

PMID:
24056632

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