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Items: 13


The recurrent architecture of tumour initiation, progression and drug sensitivity.

Califano A, Alvarez MJ.

Nat Rev Cancer. 2017 Feb;17(2):116-130. doi: 10.1038/nrc.2016.124. Epub 2016 Dec 15. Review.


Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis.

Aguiar-Pulido V, Huang W, Suarez-Ulloa V, Cickovski T, Mathee K, Narasimhan G.

Evol Bioinform Online. 2016 May 12;12(Suppl 1):5-16. doi: 10.4137/EBO.S36436. eCollection 2016. Review.


Interlog protein network: an evolutionary benchmark of protein interaction networks for the evaluation of clustering algorithms.

Jafari M, Mirzaie M, Sadeghi M.

BMC Bioinformatics. 2015 Oct 5;16:319. doi: 10.1186/s12859-015-0755-1.


Detection of composite communities in multiplex biological networks.

Bennett L, Kittas A, Muirhead G, Papageorgiou LG, Tsoka S.

Sci Rep. 2015 May 27;5:10345. doi: 10.1038/srep10345.


Porting and using PanGIA for Cytoscape 3: challenges and solutions.

Welker D, Demchak B.

F1000Res. 2014 Jul 1;3:150. doi: 10.12688/f1000research.4546.1. eCollection 2014.


Unifying immunology with informatics and multiscale biology.

Kidd BA, Peters LA, Schadt EE, Dudley JT.

Nat Immunol. 2014 Feb;15(2):118-27. doi: 10.1038/ni.2787. Review. Erratum in: Nat Immunol. 2014 Sep;15(9):894.


A UV-induced genetic network links the RSC complex to nucleotide excision repair and shows dose-dependent rewiring.

Srivas R, Costelloe T, Carvunis AR, Sarkar S, Malta E, Sun SM, Pool M, Licon K, van Welsem T, van Leeuwen F, McHugh PJ, van Attikum H, Ideker T.

Cell Rep. 2013 Dec 26;5(6):1714-24. doi: 10.1016/j.celrep.2013.11.035. Epub 2013 Dec 19.


Integrative approaches for finding modular structure in biological networks.

Mitra K, Carvunis AR, Ramesh SK, Ideker T.

Nat Rev Genet. 2013 Oct;14(10):719-32. doi: 10.1038/nrg3552. Review.


Modular biological function is most effectively captured by combining molecular interaction data types.

Ames RM, Macpherson JI, Pinney JW, Lovell SC, Robertson DL.

PLoS One. 2013 May 3;8(5):e62670. doi: 10.1371/journal.pone.0062670. Print 2013.


Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review.

Csermely P, Korcsmáros T, Kiss HJ, London G, Nussinov R.

Pharmacol Ther. 2013 Jun;138(3):333-408. doi: 10.1016/j.pharmthera.2013.01.016. Epub 2013 Feb 4. Review.


Dissection of DNA damage responses using multiconditional genetic interaction maps.

Guénolé A, Srivas R, Vreeken K, Wang ZZ, Wang S, Krogan NJ, Ideker T, van Attikum H.

Mol Cell. 2013 Jan 24;49(2):346-58. doi: 10.1016/j.molcel.2012.11.023. Epub 2012 Dec 27.


Differential analysis of high-throughput quantitative genetic interaction data.

Bean GJ, Ideker T.

Genome Biol. 2012 Dec 26;13(12):R123. doi: 10.1186/gb-2012-13-12-r123.


A travel guide to Cytoscape plugins.

Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T.

Nat Methods. 2012 Nov;9(11):1069-76. doi: 10.1038/nmeth.2212. Epub 2012 Nov 6.

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