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Results: 1 to 20 of 42

1.

The index-based subgraph matching algorithm (ISMA): fast subgraph enumeration in large networks using optimized search trees.

Demeyer S, Michoel T, Fostier J, Audenaert P, Pickavet M, Demeester P.

PLoS One. 2013 Apr 19;8(4):e61183. doi: 10.1371/journal.pone.0061183. Print 2013.

PMID:
23620730
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Network motifs provide signatures that characterize metabolism.

Shellman ER, Burant CF, Schnell S.

Mol Biosyst. 2013 Mar;9(3):352-60. doi: 10.1039/c2mb25346a. Epub 2013 Jan 4.

PMID:
23287894
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Gene regulatory network analysis supports inflammation as a key neurodegeneration process in prion disease.

Crespo I, Roomp K, Jurkowski W, Kitano H, del Sol A.

BMC Syst Biol. 2012 Oct 15;6:132. doi: 10.1186/1752-0509-6-132.

PMID:
23068602
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Motif Participation by Genes in E. coli Transcriptional Networks.

Mayo M, Abdelzaher AF, Perkins EJ, Ghosh P.

Front Physiol. 2012 Sep 24;3:357. doi: 10.3389/fphys.2012.00357. eCollection 2012.

PMID:
23055976
[PubMed]
Free PMC Article
5.

CytoKavosh: a cytoscape plug-in for finding network motifs in large biological networks.

Masoudi-Nejad A, Ansariola M, Kashani ZR, Salehzadeh-Yazdi A, Khakabimamaghani S.

PLoS One. 2012;7(8):e43287. doi: 10.1371/journal.pone.0043287. Epub 2012 Aug 29.

PMID:
22952659
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Evolutionary conservation and network structure characterize genes of phenotypic relevance for mitosis in human.

Ostaszewski M, Eifes S, del Sol A.

PLoS One. 2012;7(5):e36488. doi: 10.1371/journal.pone.0036488. Epub 2012 May 2.

PMID:
22577488
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Biological network motif detection: principles and practice.

Wong E, Baur B, Quader S, Huang CH.

Brief Bioinform. 2012 Mar;13(2):202-15. doi: 10.1093/bib/bbr033. Epub 2011 Jun 20.

PMID:
22396487
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Interplay between gene expression noise and regulatory network architecture.

Chalancon G, Ravarani CN, Balaji S, Martinez-Arias A, Aravind L, Jothi R, Babu MM.

Trends Genet. 2012 May;28(5):221-32. doi: 10.1016/j.tig.2012.01.006. Epub 2012 Feb 25. Review.

PMID:
22365642
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Delineation of key regulatory elements identifies points of vulnerability in the mitogen-activated signaling network.

Jailkhani N, Ravichandran S, Hegde SR, Siddiqui Z, Mande SC, Rao KV.

Genome Res. 2011 Dec;21(12):2067-81. doi: 10.1101/gr.116145.110. Epub 2011 Aug 24.

PMID:
21865350
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Regulation of central metabolism genes of Mycobacterium tuberculosis by parallel feed-forward loops controlled by sigma factor E (σ(E)).

Datta P, Shi L, Bibi N, Balázsi G, Gennaro ML.

J Bacteriol. 2011 Mar;193(5):1154-60. doi: 10.1128/JB.00459-10. Epub 2010 Dec 30.

PMID:
21193605
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Composite functional module inference: detecting cooperation between transcriptional regulation and protein interaction by mantel test.

Wu C, Zhang F, Li X, Zhang S, Li J, Su F, Li K, Yan Y.

BMC Syst Biol. 2010 Jun 10;4:82. doi: 10.1186/1752-0509-4-82.

PMID:
20534172
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

An interaction-motif-based scoring function for protein-ligand docking.

Xie ZR, Hwang MJ.

BMC Bioinformatics. 2010 Jun 2;11:298. doi: 10.1186/1471-2105-11-298.

PMID:
20525216
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Process-based network decomposition reveals backbone motif structure.

Wang G, Du C, Chen H, Simha R, Rong Y, Xiao Y, Zeng C.

Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10478-83. doi: 10.1073/pnas.0914180107. Epub 2010 May 24.

PMID:
20498084
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Characterizing regulatory path motifs in integrated networks using perturbational data.

Joshi A, Van Parys T, Peer YV, Michoel T.

Genome Biol. 2010;11(3):R32. doi: 10.1186/gb-2010-11-3-r32. Epub 2010 Mar 11.

PMID:
20230615
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Network inference and network response identification: moving genome-scale data to the next level of biological discovery.

Veiga DF, Dutta B, Balázsi G.

Mol Biosyst. 2010 Mar;6(3):469-80. doi: 10.1039/b916989j. Epub 2009 Dec 11. Review.

PMID:
20174676
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Functional states of the genome-scale Escherichia coli transcriptional regulatory system.

Gianchandani EP, Joyce AR, Palsson BØ, Papin JA.

PLoS Comput Biol. 2009 Jun;5(6):e1000403. doi: 10.1371/journal.pcbi.1000403. Epub 2009 Jun 5.

PMID:
19503608
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

An approach to evaluate the topological significance of motifs and other patterns in regulatory networks.

Goemann B, Wingender E, Potapov AP.

BMC Syst Biol. 2009 May 19;3:53. doi: 10.1186/1752-0509-3-53.

PMID:
19454001
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Transcriptional regulation shapes the organization of genes on bacterial chromosomes.

Janga SC, Salgado H, Martínez-Antonio A.

Nucleic Acids Res. 2009 Jun;37(11):3680-8. doi: 10.1093/nar/gkp231. Epub 2009 Apr 16.

PMID:
19372274
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

What determines the assembly of transcriptional network motifs in Escherichia coli?

Camas FM, Poyatos JF.

PLoS One. 2008;3(11):e3657. doi: 10.1371/journal.pone.0003657. Epub 2008 Nov 6.

PMID:
18987754
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Functional architecture of Escherichia coli: new insights provided by a natural decomposition approach.

Freyre-González JA, Alonso-Pavón JA, Treviño-Quintanilla LG, Collado-Vides J.

Genome Biol. 2008 Oct 27;9(10):R154. doi: 10.1186/gb-2008-9-10-r154.

PMID:
18954463
[PubMed - indexed for MEDLINE]
Free PMC Article

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