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Results: 1 to 20 of 83

1.

attract: A method for identifying core pathways that define cellular phenotypes.

Mar JC, Matigian NA, Quackenbush J, Wells CA.

PLoS One. 2011;6(10):e25445. doi: 10.1371/journal.pone.0025445. Epub 2011 Oct 14.

PMID:
22022396
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Investigating meta-approaches for reconstructing gene networks in a mammalian cellular context.

Nazri A, Lio P.

PLoS One. 2012;7(1):e28713. doi: 10.1371/journal.pone.0028713. Epub 2012 Jan 9.

PMID:
22253694
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Systematic identification of gene annotation errors in the widely used yeast mutation collections.

Ben-Shitrit T, Yosef N, Shemesh K, Sharan R, Ruppin E, Kupiec M.

Nat Methods. 2012 Feb 5;9(4):373-8. doi: 10.1038/nmeth.1890.

PMID:
22306811
[PubMed - indexed for MEDLINE]
4.

SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks.

Westenberg MA, Roerdink JB, Kuipers OP, van Hijum SA.

Bioinformatics. 2010 Nov 15;26(22):2922-3. doi: 10.1093/bioinformatics/btq535. Epub 2010 Sep 21.

PMID:
20861033
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations.

Castro MA, Wang X, Fletcher MN, Meyer KB, Markowetz F.

Genome Biol. 2012 Apr 24;13(4):R29. doi: 10.1186/gb-2012-13-4-r29.

PMID:
22531049
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

VitisNet: "Omics" integration through grapevine molecular networks.

Grimplet J, Cramer GR, Dickerson JA, Mathiason K, Van Hemert J, Fennell AY.

PLoS One. 2009 Dec 21;4(12):e8365. doi: 10.1371/journal.pone.0008365.

PMID:
20027228
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Delineation and interpretation of gene networks towards their effect in cellular physiology- a reverse engineering approach for the identification of critical molecular players, through the use of ontologies.

Moutselos K, Maglogiannis I, Chatziioannou A.

Conf Proc IEEE Eng Med Biol Soc. 2010;2010:6709-12. doi: 10.1109/IEMBS.2010.5626249.

PMID:
21096082
[PubMed - indexed for MEDLINE]
8.

KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor.

Zhang JD, Wiemann S.

Bioinformatics. 2009 Jun 1;25(11):1470-1. doi: 10.1093/bioinformatics/btp167. Epub 2009 Mar 23.

PMID:
19307239
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Browsing metabolic and regulatory networks with BioCyc.

Latendresse M, Paley S, Karp PD.

Methods Mol Biol. 2012;804:197-216. doi: 10.1007/978-1-61779-361-5_11.

PMID:
22144155
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Construction of coffee transcriptome networks based on gene annotation semantics.

Castillo LF, Galeano N, Isaza GA, Gaitán A.

J Integr Bioinform. 2012 Jul 24;9(3):205. doi: 10.2390/biecoll-jib-2012-205.

PMID:
22829576
[PubMed - indexed for MEDLINE]
11.

Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network.

Aho T, Almusa H, Matilainen J, Larjo A, Ruusuvuori P, Aho KL, Wilhelm T, Lähdesmäki H, Beyer A, Harju M, Chowdhury S, Leinonen K, Roos C, Yli-Harja O.

PLoS One. 2010 May 14;5(5):e10662. doi: 10.1371/journal.pone.0010662.

PMID:
20498836
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

EGAN: exploratory gene association networks.

Paquette J, Tokuyasu T.

Bioinformatics. 2010 Jan 15;26(2):285-6. doi: 10.1093/bioinformatics/btp656. Epub 2009 Nov 23.

PMID:
19933825
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

NuChart: an R package to study gene spatial neighbourhoods with multi-omics annotations.

Merelli I, Liò P, Milanesi L.

PLoS One. 2013 Sep 19;8(9):e75146. doi: 10.1371/journal.pone.0075146. eCollection 2013.

PMID:
24069388
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

VisANT: an online visualization and analysis tool for biological interaction data.

Hu Z, Mellor J, Wu J, DeLisi C.

BMC Bioinformatics. 2004 Feb 19;5:17.

PMID:
15028117
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

WGCNA: an R package for weighted correlation network analysis.

Langfelder P, Horvath S.

BMC Bioinformatics. 2008 Dec 29;9:559. doi: 10.1186/1471-2105-9-559.

PMID:
19114008
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Graph constrained discriminant analysis: a new method for the integration of a graph into a classification process.

Guillemot V, Tenenhaus A, Le Brusquet L, Frouin V.

PLoS One. 2011;6(10):e26146. doi: 10.1371/journal.pone.0026146. Epub 2011 Oct 14.

PMID:
22022543
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Towards integrative annotation of the cell-type specific gene functional and signaling map in vascular endothelial cells.

Gu J, Li S.

Mol Biosyst. 2012 Aug;8(8):2041-9. doi: 10.1039/c2mb25065a. Epub 2012 Jun 1.

PMID:
22660772
[PubMed - indexed for MEDLINE]
18.

PathGen: a transitive gene pathway generator.

Clement K, Gustafson N, Berbert A, Carroll H, Merris C, Olsen A, Clement M, Snell Q, Allen J, Roper RJ.

Bioinformatics. 2010 Feb 1;26(3):423-5. doi: 10.1093/bioinformatics/btp661. Epub 2009 Dec 4.

PMID:
19965882
[PubMed - indexed for MEDLINE]
Free Article
19.

Inherited disorder phenotypes: controlled annotation and statistical analysis for knowledge mining from gene lists.

Masseroli M, Galati O, Manzotti M, Gibert K, Pinciroli F.

BMC Bioinformatics. 2005 Dec 1;6 Suppl 4:S18.

PMID:
16351744
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Computational annotation of genes differentially expressed along olive fruit development.

Galla G, Barcaccia G, Ramina A, Collani S, Alagna F, Baldoni L, Cultrera NG, Martinelli F, Sebastiani L, Tonutti P.

BMC Plant Biol. 2009 Oct 24;9:128. doi: 10.1186/1471-2229-9-128.

PMID:
19852839
[PubMed - indexed for MEDLINE]
Free PMC Article

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