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Items: 15

1.

TNF-insulin crosstalk at the transcription factor GATA6 is revealed by a model that links signaling and transcriptomic data tensors.

Chitforoushzadeh Z, Ye Z, Sheng Z, LaRue S, Fry RC, Lauffenburger DA, Janes KA.

Sci Signal. 2016 Jun 7;9(431):ra59. doi: 10.1126/scisignal.aad3373.

PMID:
27273097
2.

Data- and knowledge-based modeling of gene regulatory networks: an update.

Linde J, Schulze S, Henkel SG, Guthke R.

EXCLI J. 2015 Mar 2;14:346-78. doi: 10.17179/excli2015-168. Review.

3.

Phosphatase specificity and pathway insulation in signaling networks.

Rowland MA, Harrison B, Deeds EJ.

Biophys J. 2015 Feb 17;108(4):986-96. doi: 10.1016/j.bpj.2014.12.011.

4.

Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease.

Yang HJ, Ratnapriya R, Cogliati T, Kim JW, Swaroop A.

Prog Retin Eye Res. 2015 May;46:1-30. doi: 10.1016/j.preteyeres.2015.01.005. Review.

5.

In silico model-based inference: a contemporary approach for hypothesis testing in network biology.

Klinke DJ 2nd.

Biotechnol Prog. 2014 Nov-Dec;30(6):1247-61. doi: 10.1002/btpr.1982.

6.

Using biological pathway data with paxtools.

Demir E, Babur O, Rodchenkov I, Aksoy BA, Fukuda KI, Gross B, Sümer OS, Bader GD, Sander C.

PLoS Comput Biol. 2013;9(9):e1003194. doi: 10.1371/journal.pcbi.1003194.

7.

Quantifying crosstalk among interferon-γ, interleukin-12, and tumor necrosis factor signaling pathways within a TH1 cell model.

Klinke DJ 2nd, Cheng N, Chambers E.

Sci Signal. 2012 Apr 17;5(220):ra32. doi: 10.1126/scisignal.2002657.

8.
9.

So what do we really mean when we say that systems biology is holistic?

Gatherer D.

BMC Syst Biol. 2010 Mar 12;4:22. doi: 10.1186/1752-0509-4-22. Review.

10.

Networks and pathways in pigmentation, health, and disease.

Baxter LL, Loftus SK, Pavan WJ.

Wiley Interdiscip Rev Syst Biol Med. 2009 Nov-Dec;1(3):359-71. doi: 10.1002/wsbm.20. Review.

11.

Computational systems biology in cancer: modeling methods and applications.

Materi W, Wishart DS.

Gene Regul Syst Bio. 2007 Sep 17;1:91-110.

12.

Systemic darwinism.

Winther RG.

Proc Natl Acad Sci U S A. 2008 Aug 19;105(33):11833-8. doi: 10.1073/pnas.0711445105.

13.

Understanding diseases by mouse click: the promise and potential of computational approaches in Systems Biology.

Klauschen F, Angermann BR, Meier-Schellersheim M.

Clin Exp Immunol. 2007 Sep;149(3):424-9. Review.

14.
15.

Sepsis progression and outcome: a dynamical model.

Zuev SM, Kingsmore SF, Gessler DD.

Theor Biol Med Model. 2006 Feb 15;3:8.

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