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Dynamic protein-protein interaction subnetworks of lung cancer in cases with smoking history.

Yu W, He LR, Zhao YC, Chan MH, Zhang M, He M.

Chin J Cancer. 2013 Feb;32(2):84-90. doi: 10.5732/cjc.012.10099. Epub 2012 Nov 13.


Module organization and variance in protein-protein interaction networks.

Lin CY, Lee TL, Chiu YY, Lin YW, Lo YS, Lin CT, Yang JM.

Sci Rep. 2015 Mar 23;5:9386. doi: 10.1038/srep09386.


Assessment of subnetwork detection methods for breast cancer.

Jiang B, Gribskov M.

Cancer Inform. 2014 Dec 2;13(Suppl 6):15-23. doi: 10.4137/CIN.S17641. eCollection 2014.


Analysis and identification of toxin targets by topological properties in protein-protein interaction network.

Yang L, Wang J, Wang H, Lv Y, Zuo Y, Jiang W.

J Theor Biol. 2014 May 21;349:82-91. doi: 10.1016/j.jtbi.2014.02.001. Epub 2014 Feb 7.


Integrating structure to protein-protein interaction networks that drive metastasis to brain and lung in breast cancer.

Engin HB, Guney E, Keskin O, Oliva B, Gursoy A.

PLoS One. 2013 Nov 22;8(11):e81035. doi: 10.1371/journal.pone.0081035. eCollection 2013.


Identification of highly synchronized subnetworks from gene expression data.

Gao S, Wang X.

BMC Bioinformatics. 2013;14 Suppl 9:S5. doi: 10.1186/1471-2105-14-S9-S5. Epub 2013 Jun 28.


Prediction of protein-protein interactions from amino acid sequences with ensemble extreme learning machines and principal component analysis.

You ZH, Lei YK, Zhu L, Xia J, Wang B.

BMC Bioinformatics. 2013;14 Suppl 8:S10. doi: 10.1186/1471-2105-14-S8-S10. Epub 2013 May 9.


Extracting a few functionally reproducible biomarkers to build robust subnetwork-based classifiers for the diagnosis of cancer.

Zhang L, Li S, Hao C, Hong G, Zou J, Zhang Y, Li P, Guo Z.

Gene. 2013 Sep 10;526(2):232-8. doi: 10.1016/j.gene.2013.05.011. Epub 2013 May 22.


Activation of Akt pathway by transcription-independent mechanisms of retinoic acid promotes survival and invasion in lung cancer cells.

García-Regalado A, Vargas M, García-Carrancá A, Aréchaga-Ocampo E, González-De la Rosa CH.

Mol Cancer. 2013 May 21;12:44. doi: 10.1186/1476-4598-12-44.


Imputation-based association analyses identify new lung cancer susceptibility variants in CDK6 and SH3RF1 and their interactions with smoking in Chinese populations.

Deng Q, Guo H, Dai J, Yang L, Wu C, Wang Q, Hu Z, Yang M, Liu L, Yu D, Hu D, Hong X, Qiu F, Yang H, Wang T, Tan W, Chu M, Feng J, Teng K, Gong J, Sun C, Hu X, Zhang K, Lu J, Lin D, Shen H, Wu T.

Carcinogenesis. 2013 Sep;34(9):2010-6. doi: 10.1093/carcin/bgt145. Epub 2013 May 3.


t-LSE: a novel robust geometric approach for modeling protein-protein interaction networks.

Zhu L, You ZH, Huang DS, Wang B.

PLoS One. 2013;8(4):e58368. doi: 10.1371/journal.pone.0058368. Epub 2013 Apr 1.


Dynamic circadian protein-protein interaction networks predict temporal organization of cellular functions.

Wallach T, Schellenberg K, Maier B, Kalathur RK, Porras P, Wanker EE, Futschik ME, Kramer A.

PLoS Genet. 2013 Mar;9(3):e1003398. doi: 10.1371/journal.pgen.1003398. Epub 2013 Mar 28.


Active subnetwork recovery with a mechanism-dependent scoring function; with application to angiogenesis and organogenesis studies.

Lichtenstein I, Charleston MA, Caetano TS, Gamble JR, Vadas MA.

BMC Bioinformatics. 2013 Feb 21;14:59. doi: 10.1186/1471-2105-14-59.


Visualization of protein interaction networks: problems and solutions.

Agapito G, Guzzi PH, Cannataro M.

BMC Bioinformatics. 2013;14 Suppl 1:S1. doi: 10.1186/1471-2105-14-S1-S1. Epub 2013 Jan 14.


Protocadherin 10 is frequently downregulated by promoter methylation and functions as a tumor suppressor gene in non-small cell lung cancer.

Tang X, Yin X, Xiang T, Li H, Li F, Chen L, Ren G.

Cancer Biomark. 2012-2013;12(1):11-9. doi: 10.3233/CBM-2012-00280.


Adding protein context to the human protein-protein interaction network to reveal meaningful interactions.

Schaefer MH, Lopes TJ, Mah N, Shoemaker JE, Matsuoka Y, Fontaine JF, Louis-Jeune C, Eisfeld AJ, Neumann G, Perez-Iratxeta C, Kawaoka Y, Kitano H, Andrade-Navarro MA.

PLoS Comput Biol. 2013;9(1):e1002860. doi: 10.1371/journal.pcbi.1002860. Epub 2013 Jan 3.


PCDq: human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from h-invitational protein-protein interactions integrative dataset.

Kikugawa S, Nishikata K, Murakami K, Sato Y, Suzuki M, Altaf-Ul-Amin M, Kanaya S, Imanishi T.

BMC Syst Biol. 2012;6 Suppl 2:S7. doi: 10.1186/1752-0509-6-S2-S7. Epub 2012 Dec 12.


Using the theory of coevolution to predict protein-protein interactions in non-small cell lung cancer.

Zhang M, Chan MH, Tu WJ, He LR, Lee CM, He M.

Chin J Cancer. 2013 Feb;32(2):91-8. doi: 10.5732/cjc.012.10100. Epub 2012 Dec 14.


The TissueNet database of human tissue protein-protein interactions.

Barshir R, Basha O, Eluk A, Smoly IY, Lan A, Yeger-Lotem E.

Nucleic Acids Res. 2013 Jan;41(Database issue):D841-4. doi: 10.1093/nar/gks1198. Epub 2012 Nov 27.


Coevolution reveals a network of human proteins originating with multicellularity.

Bezginov A, Clark GW, Charlebois RL, Dar VU, Tillier ER.

Mol Biol Evol. 2013 Feb;30(2):332-46. doi: 10.1093/molbev/mss218. Epub 2012 Sep 12.

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