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Pathway Interaction Network Analysis Identifies Dysregulated Pathways in Human Monocytes Infected by Listeria monocytogenes.

Fan W, Zhou Y, Li H.

Comput Math Methods Med. 2017;2017:3195348. doi: 10.1155/2017/3195348. Epub 2017 Aug 16.


NetGen: a novel network-based probabilistic generative model for gene set functional enrichment analysis.

Sun D, Liu Y, Zhang XS, Wu LY.

BMC Syst Biol. 2017 Sep 21;11(Suppl 4):75. doi: 10.1186/s12918-017-0456-7.


Identification of gene markers associated with metastasis in clear cell renal cell carcinoma.

Yang H, Huo P, Hu G, Wei B, Kong D, Li H.

Oncol Lett. 2017 Jun;13(6):4755-4761. doi: 10.3892/ol.2017.6084. Epub 2017 Apr 24.


Identification of target genes of cediranib in alveolar soft part sarcoma using a gene microarray.

Jiang W, Liu P, Li X, Wang P.

Oncol Lett. 2017 Apr;13(4):2623-2630. doi: 10.3892/ol.2017.5779. Epub 2017 Feb 24.


Benchmarking pathway interaction network for colorectal cancer to identify dysregulated pathways.

Wang Q, Shi CJ, Lv SH.

Braz J Med Biol Res. 2017 Mar 30;50(5):e5981. doi: 10.1590/1414-431X20175981.


Multipronged Therapeutic Effects of Chinese Herbal Medicine Qishenyiqi in the Treatment of Acute Myocardial Infarction.

Wang Y, Lin W, Li C, Singhal S, Jain G, Zhu L, Lu L, Zhu R, Wang W.

Front Pharmacol. 2017 Mar 2;8:98. doi: 10.3389/fphar.2017.00098. eCollection 2017.


Post-transcriptional knowledge in pathway analysis increases the accuracy of phenotypes classification.

Alaimo S, Giugno R, Acunzo M, Veneziano D, Ferro A, Pulvirenti A.

Oncotarget. 2016 Aug 23;7(34):54572-54582. doi: 10.18632/oncotarget.9788.


Application of biclustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials.

Williams A, Halappanavar S.

Beilstein J Nanotechnol. 2015 Dec 21;6:2438-48. doi: 10.3762/bjnano.6.252. eCollection 2015.


Gene set enrichment and topological analyses based on interaction networks in pediatric acute lymphoblastic leukemia.

Sui S, Wang X, Zheng H, Guo H, Chen T, Ji DM.

Oncol Lett. 2015 Dec;10(6):3354-3362. Epub 2015 Sep 29.


Western-style diet, with and without chronic androgen treatment, alters the number, structure, and function of small antral follicles in ovaries of young adult monkeys.

Bishop CV, Xu F, Xu J, Ting AY, Galbreath E, McGee WK, Zelinski MB, Hennebold JD, Cameron JL, Stouffer RL.

Fertil Steril. 2016 Apr;105(4):1023-34. doi: 10.1016/j.fertnstert.2015.11.045. Epub 2015 Dec 21.


ΔNp63α induces quiescence and downregulates the BRCA1 pathway in estrogen receptor-positive luminal breast cancer cell line MCF7 but not in other breast cancer cell lines.

Amin R, Morita-Fujimura Y, Tawarayama H, Semba K, Chiba N, Fukumoto M, Ikawa S.

Mol Oncol. 2016 Apr;10(4):575-93. doi: 10.1016/j.molonc.2015.11.009. Epub 2015 Nov 24.


Human Gene Expression in Uncomplicated Plasmodium falciparum Malaria.

Colborn JM, Ylöstalo JH, Koita OA, Cissé OH, Krogstad DJ.

J Immunol Res. 2015;2015:162639. doi: 10.1155/2015/162639. Epub 2015 Sep 30.


Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment.

Bohler A, Eijssen LM, van Iersel MP, Leemans C, Willighagen EL, Kutmon M, Jaillard M, Evelo CT.

BMC Bioinformatics. 2015 Aug 23;16:267. doi: 10.1186/s12859-015-0708-8.


ExAtlas: An interactive online tool for meta-analysis of gene expression data.

Sharov AA, Schlessinger D, Ko MS.

J Bioinform Comput Biol. 2015 Dec;13(6):1550019. doi: 10.1142/S0219720015500195. Epub 2015 Jun 9.


PathVisio 3: an extendable pathway analysis toolbox.

Kutmon M, van Iersel MP, Bohler A, Kelder T, Nunes N, Pico AR, Evelo CT.

PLoS Comput Biol. 2015 Feb 23;11(2):e1004085. doi: 10.1371/journal.pcbi.1004085. eCollection 2015 Feb.


Hierarchy in gene expression is predictive of risk, progression, and outcome in adult acute myeloid leukemia.

Tripathi S, Deem MW.

Phys Biol. 2015 Feb 16;12(1):016016. doi: 10.1088/1478-3975/12/1/016016.


Stage-specific signaling pathways during murine testis development and spermatogenesis: A pathway-based analysis to quantify developmental dynamics.

Wegner SH, Yu X, Pacheco Shubin S, Griffith WC, Faustman EM.

Reprod Toxicol. 2015 Jan;51:31-9. doi: 10.1016/j.reprotox.2014.11.008. Epub 2014 Nov 25.


A network biology workflow to study transcriptomics data of the diabetic liver.

Kutmon M, Evelo CT, Coort SL.

BMC Genomics. 2014 Nov 15;15:971. doi: 10.1186/1471-2164-15-971.


Learning dysregulated pathways in cancers from differential variability analysis.

Afsari B, Geman D, Fertig EJ.

Cancer Inform. 2014 Oct 23;13(Suppl 5):61-7. doi: 10.4137/CIN.S14066. eCollection 2014. Review.

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