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Items: 12

1.

Integration of biological networks and gene expression data using Cytoscape.

Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD.

Nat Protoc. 2007;2(10):2366-82.

2.

Biological Network Inference and analysis using SEBINI and CABIN.

Taylor R, Singhal M.

Methods Mol Biol. 2009;541:551-76. doi: 10.1007/978-1-59745-243-4_24. Review.

PMID:
19381531
3.

Functional genomics and proteomics in the clinical neurosciences: data mining and bioinformatics.

Phan JH, Quo CF, Wang MD.

Prog Brain Res. 2006;158:83-108. Review.

PMID:
17027692
4.

A survey of current software for network analysis in molecular biology.

Thomas S, Bonchev D.

Hum Genomics. 2010 Jun;4(5):353-60. Review.

5.

Inference of dynamic networks using time-course data.

Kim Y, Han S, Choi S, Hwang D.

Brief Bioinform. 2014 Mar;15(2):212-28. doi: 10.1093/bib/bbt028. Epub 2013 May 21. Review.

PMID:
23698724
6.

Pathway and network analysis in proteomics.

Wu X, Hasan MA, Chen JY.

J Theor Biol. 2014 Dec 7;362:44-52. doi: 10.1016/j.jtbi.2014.05.031. Epub 2014 Jun 6. Review.

7.

Using biological networks to integrate, visualize and analyze genomics data.

Charitou T, Bryan K, Lynn DJ.

Genet Sel Evol. 2016 Mar 31;48:27. doi: 10.1186/s12711-016-0205-1. Review.

8.

Processing, visualising and reconstructing network models from single-cell data.

Woodhouse S, Moignard V, Göttgens B, Fisher J.

Immunol Cell Biol. 2016 Mar;94(3):256-65. doi: 10.1038/icb.2015.102. Epub 2015 Nov 18. Review.

PMID:
26577213
9.

Principles and methods of integrative genomic analyses in cancer.

Kristensen VN, Lingjærde OC, Russnes HG, Vollan HK, Frigessi A, Børresen-Dale AL.

Nat Rev Cancer. 2014 May;14(5):299-313. doi: 10.1038/nrc3721. Review.

PMID:
24759209
10.

Network propagation: a universal amplifier of genetic associations.

Cowen L, Ideker T, Raphael BJ, Sharan R.

Nat Rev Genet. 2017 Sep;18(9):551-562. doi: 10.1038/nrg.2017.38. Epub 2017 Jun 12. Review.

PMID:
28607512
11.

A new toolbox for assessing single cells.

Tsioris K, Torres AJ, Douce TB, Love JC.

Annu Rev Chem Biomol Eng. 2014;5:455-77. doi: 10.1146/annurev-chembioeng-060713-035958. Review.

12.

Decoding neuroproteomics: integrating the genome, translatome and functional anatomy.

Kitchen RR, Rozowsky JS, Gerstein MB, Nairn AC.

Nat Neurosci. 2014 Nov;17(11):1491-9. doi: 10.1038/nn.3829. Epub 2014 Oct 28. Review.

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