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Results: 1 to 20 of 101

1.

Cross-species cluster co-conservation: a new method for generating protein interaction networks.

Karimpour-Fard A, Detweiler CS, Erickson KD, Hunter L, Gill RT.

Genome Biol. 2007;8(9):R185.

PMID:
17803817
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

The topology of the bacterial co-conserved protein network and its implications for predicting protein function.

Karimpour-Fard A, Leach SM, Hunter LE, Gill RT.

BMC Genomics. 2008 Jun 30;9:313. doi: 10.1186/1471-2164-9-313.

PMID:
18590549
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Inferring modules of functionally interacting proteins using the Bond Energy Algorithm.

Watanabe RL, Morett E, Vallejo EE.

BMC Bioinformatics. 2008 Jun 17;9:285. doi: 10.1186/1471-2105-9-285.

PMID:
18559112
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Resolving the structure of interactomes with hierarchical agglomerative clustering.

Park Y, Bader JS.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S44. doi: 10.1186/1471-2105-12-S1-S44.

PMID:
21342576
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Investigation of factors affecting prediction of protein-protein interaction networks by phylogenetic profiling.

Karimpour-Fard A, Hunter L, Gill RT.

BMC Genomics. 2007 Oct 29;8:393.

PMID:
17967189
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

The comparative genomics of protein interactions.

Peregrín-Alvarez JM, Ouzounis CA.

Genome Inform. 2007;19:131-41.

PMID:
18546511
[PubMed - indexed for MEDLINE]
7.

Finding molecular complexes through multiple layer clustering of protein interaction networks.

Andreopoulos B, An A, Huang X, Wang X.

Int J Bioinform Res Appl. 2007;3(1):65-85.

PMID:
18048173
[PubMed - indexed for MEDLINE]
8.

The use of edge-betweenness clustering to investigate biological function in protein interaction networks.

Dunn R, Dudbridge F, Sanderson CM.

BMC Bioinformatics. 2005 Mar 1;6:39.

PMID:
15740614
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Editorial: protein systems biology: method, regulation, and network.

Chen Q, Chen M.

Curr Protein Pept Sci. 2014;15(6):519-21.

PMID:
25135673
[PubMed - in process]
10.

Evolutionary cores of domain co-occurrence networks.

Wuchty S, Almaas E.

BMC Evol Biol. 2005 Mar 23;5:24.

PMID:
15788102
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Identifying conserved protein complexes between species by constructing interolog networks.

Nguyen PV, Srihari S, Leong HW.

BMC Bioinformatics. 2013;14 Suppl 16:S8. doi: 10.1186/1471-2105-14-S16-S8. Epub 2013 Oct 22.

PMID:
24564762
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Detection of functional modules from protein interaction networks with an enhanced random walk based algorithm.

Cai B, Wang H, Zheng H, Wang H.

Int J Comput Biol Drug Des. 2011;4(3):290-306. doi: 10.1504/IJCBDD.2011.041416. Epub 2011 Jul 21.

PMID:
21778561
[PubMed - indexed for MEDLINE]
13.

Non-linear mapping for exploratory data analysis in functional genomics.

Azuaje F, Wang H, Chesneau A.

BMC Bioinformatics. 2005 Jan 20;6:13.

PMID:
15661072
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Inferring functional information from domain co-evolution.

Kim Y, Koyutürk M, Topkara U, Grama A, Subramaniam S.

Bioinformatics. 2006 Jan 1;22(1):40-9. Epub 2005 Nov 13.

PMID:
16301205
[PubMed - indexed for MEDLINE]
Free Article
15.

Revealing biological modules via graph summarization.

Navlakha S, Schatz MC, Kingsford C.

J Comput Biol. 2009 Feb;16(2):253-64. doi: 10.1089/cmb.2008.11TT.

PMID:
19183002
[PubMed - indexed for MEDLINE]
16.
17.

How and when should interactome-derived clusters be used to predict functional modules and protein function?

Song J, Singh M.

Bioinformatics. 2009 Dec 1;25(23):3143-50. doi: 10.1093/bioinformatics/btp551. Epub 2009 Sep 21.

PMID:
19770263
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Phylogenetic analysis of modularity in protein interaction networks.

Erten S, Li X, Bebek G, Li J, Koyutürk M.

BMC Bioinformatics. 2009 Oct 14;10:333. doi: 10.1186/1471-2105-10-333.

PMID:
19828041
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Biological networks: comparison, conservation, and evolution via relative description length.

Chor B, Tuller T.

J Comput Biol. 2007 Jul-Aug;14(6):817-38.

PMID:
17691896
[PubMed - indexed for MEDLINE]
20.

Bayesian coestimation of phylogeny and sequence alignment.

Lunter G, Miklós I, Drummond A, Jensen JL, Hein J.

BMC Bioinformatics. 2005 Apr 1;6:83.

PMID:
15804354
[PubMed - indexed for MEDLINE]
Free PMC Article

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