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Items: 1 to 20 of 105

1.

Statistical assessment of crosstalk enrichment between gene groups in biological networks.

McCormack T, Frings O, Alexeyenko A, Sonnhammer EL.

PLoS One. 2013;8(1):e54945. doi: 10.1371/journal.pone.0054945. Epub 2013 Jan 23.

2.

A novel method for crosstalk analysis of biological networks: improving accuracy of pathway annotation.

Ogris C, Guala D, Helleday T, Sonnhammer EL.

Nucleic Acids Res. 2017 Jan 25;45(2):e8. doi: 10.1093/nar/gkw849. Epub 2016 Sep 22.

3.

Differential regulation enrichment analysis via the integration of transcriptional regulatory network and gene expression data.

Ma S, Jiang T, Jiang R.

Bioinformatics. 2015 Feb 15;31(4):563-71. doi: 10.1093/bioinformatics/btu672. Epub 2014 Oct 15.

PMID:
25322838
4.

NET-GE: a novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseases.

Di Lena P, Martelli PL, Fariselli P, Casadio R.

BMC Genomics. 2015;16 Suppl 8:S6. doi: 10.1186/1471-2164-16-S8-S6. Epub 2015 Jun 18.

5.

Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph.

Richards AJ, Muller B, Shotwell M, Cowart LA, Rohrer B, Lu X.

Bioinformatics. 2010 Jun 15;26(12):i79-87. doi: 10.1093/bioinformatics/btq203.

6.

Enrichment map: a network-based method for gene-set enrichment visualization and interpretation.

Merico D, Isserlin R, Stueker O, Emili A, Bader GD.

PLoS One. 2010 Nov 15;5(11):e13984. doi: 10.1371/journal.pone.0013984.

7.

A novel dysregulated pathway-identification analysis based on global influence of within-pathway effects and crosstalk between pathways.

Han J, Li C, Yang H, Xu Y, Zhang C, Ma J, Shi X, Liu W, Shang D, Yao Q, Zhang Y, Su F, Feng L, Li X.

J R Soc Interface. 2015 Jan 6;12(102):20140937.

8.

Xtalk: a path-based approach for identifying crosstalk between signaling pathways.

Tegge AN, Sharp N, Murali TM.

Bioinformatics. 2016 Jan 15;32(2):242-51. doi: 10.1093/bioinformatics/btv549. Epub 2015 Sep 23.

9.

Network enrichment analysis: extension of gene-set enrichment analysis to gene networks.

Alexeyenko A, Lee W, Pernemalm M, Guegan J, Dessen P, Lazar V, Lehtiƶ J, Pawitan Y.

BMC Bioinformatics. 2012 Sep 11;13:226. doi: 10.1186/1471-2105-13-226.

10.

NOA: a novel Network Ontology Analysis method.

Wang J, Huang Q, Liu ZP, Wang Y, Wu LY, Chen L, Zhang XS.

Nucleic Acids Res. 2011 Jul;39(13):e87. doi: 10.1093/nar/gkr251. Epub 2011 May 4.

11.

Inference of biological pathway from gene expression profiles by time delay boolean networks.

Chueh TH, Lu HH.

PLoS One. 2012;7(8):e42095. doi: 10.1371/journal.pone.0042095. Epub 2012 Aug 31.

12.

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
13.

Discriminating response groups in metabolic and regulatory pathway networks.

Van Hemert JL, Dickerson JA.

Bioinformatics. 2012 Apr 1;28(7):947-54. doi: 10.1093/bioinformatics/bts039. Epub 2012 Feb 4.

PMID:
22308149
14.

FunRich: An open access standalone functional enrichment and interaction network analysis tool.

Pathan M, Keerthikumar S, Ang CS, Gangoda L, Quek CY, Williamson NA, Mouradov D, Sieber OM, Simpson RJ, Salim A, Bacic A, Hill AF, Stroud DA, Ryan MT, Agbinya JI, Mariadason JM, Burgess AW, Mathivanan S.

Proteomics. 2015 Aug;15(15):2597-601. doi: 10.1002/pmic.201400515. Epub 2015 Jun 17.

PMID:
25921073
15.

Robust identification of transcriptional regulatory networks using a Gibbs sampler on outlier sum statistic.

Gu J, Xuan J, Riggins RB, Chen L, Wang Y, Clarke R.

Bioinformatics. 2012 Aug 1;28(15):1990-7. doi: 10.1093/bioinformatics/bts296. Epub 2012 May 17. Erratum in: Bioinformatics. 2014 Aug 1;30(15):2242.

16.

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists.

Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z.

BMC Bioinformatics. 2009 Feb 3;10:48. doi: 10.1186/1471-2105-10-48.

17.

PathwAX: a web server for network crosstalk based pathway annotation.

Ogris C, Helleday T, Sonnhammer EL.

Nucleic Acids Res. 2016 Jul 8;44(W1):W105-9. doi: 10.1093/nar/gkw356. Epub 2016 May 5.

18.

Characterizing the topology of probabilistic biological networks.

Todor A, Dobra A, Kahveci T.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Jul-Aug;10(4):970-83. doi: 10.1109/TCBB.2013.108.

PMID:
24334390
19.

EnrichNet: network-based gene set enrichment analysis.

Glaab E, Baudot A, Krasnogor N, Schneider R, Valencia A.

Bioinformatics. 2012 Sep 15;28(18):i451-i457. doi: 10.1093/bioinformatics/bts389.

20.

Comparing gene annotation enrichment tools for functional modeling of agricultural microarray data.

van den Berg BH, Thanthiriwatte C, Manda P, Bridges SM.

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S9. doi: 10.1186/1471-2105-10-S11-S9.

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