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Items: 1 to 20 of 110

1.

An inter-species protein-protein interaction network across vast evolutionary distance.

Zhong Q, Pevzner SJ, Hao T, Wang Y, Mosca R, Menche J, Taipale M, Taşan M, Fan C, Yang X, Haley P, Murray RR, Mer F, Gebreab F, Tam S, MacWilliams A, Dricot A, Reichert P, Santhanam B, Ghamsari L, Calderwood MA, Rolland T, Charloteaux B, Lindquist S, Barabási AL, Hill DE, Aloy P, Cusick ME, Xia Y, Roth FP, Vidal M.

Mol Syst Biol. 2016 Apr 22;12(4):865. doi: 10.15252/msb.20156484.

2.

Identification of functional hubs and modules by converting interactome networks into hierarchical ordering of proteins.

Cho YR, Zhang A.

BMC Bioinformatics. 2010 Apr 29;11 Suppl 3:S3. doi: 10.1186/1471-2105-11-S3-S3.

3.

Predicting the interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service.

Kim JG, Park D, Kim BC, Cho SW, Kim YT, Park YJ, Cho HJ, Park H, Kim KB, Yoon KO, Park SJ, Lee BM, Bhak J.

BMC Bioinformatics. 2008 Jan 24;9:41. doi: 10.1186/1471-2105-9-41.

4.

Finding the "dark matter" in human and yeast protein network prediction and modelling.

Ranea JA, Morilla I, Lees JG, Reid AJ, Yeats C, Clegg AB, Sanchez-Jimenez F, Orengo C.

PLoS Comput Biol. 2010 Sep 23;6(9). pii: e1000945. doi: 10.1371/journal.pcbi.1000945.

5.

Evolutionary cores of domain co-occurrence networks.

Wuchty S, Almaas E.

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

6.

Network simulation reveals significant contribution of network motifs to the age-dependency of yeast protein-protein interaction networks.

Liang C, Luo J, Song D.

Mol Biosyst. 2014 Jul 29;10(9):2277-88. doi: 10.1039/c4mb00230j.

PMID:
24964354
7.

Evolutionary capacitance and control of protein stability in protein-protein interaction networks.

Dixit PD, Maslov S.

PLoS Comput Biol. 2013 Apr;9(4):e1003023. doi: 10.1371/journal.pcbi.1003023. Epub 2013 Apr 4.

8.

Influence of protein abundance on high-throughput protein-protein interaction detection.

Ivanic J, Yu X, Wallqvist A, Reifman J.

PLoS One. 2009 Jun 5;4(6):e5815. doi: 10.1371/journal.pone.0005815.

9.

Discerning molecular interactions: A comprehensive review on biomolecular interaction databases and network analysis tools.

Miryala SK, Anbarasu A, Ramaiah S.

Gene. 2018 Feb 5;642:84-94. doi: 10.1016/j.gene.2017.11.028. Epub 2017 Nov 10. Review.

PMID:
29129810
10.

WI-PHI: a weighted yeast interactome enriched for direct physical interactions.

Kiemer L, Costa S, Ueffing M, Cesareni G.

Proteomics. 2007 Mar;7(6):932-43.

PMID:
17285561
11.

Architecture of the human interactome defines protein communities and disease networks.

Huttlin EL, Bruckner RJ, Paulo JA, Cannon JR, Ting L, Baltier K, Colby G, Gebreab F, Gygi MP, Parzen H, Szpyt J, Tam S, Zarraga G, Pontano-Vaites L, Swarup S, White AE, Schweppe DK, Rad R, Erickson BK, Obar RA, Guruharsha KG, Li K, Artavanis-Tsakonas S, Gygi SP, Harper JW.

Nature. 2017 May 25;545(7655):505-509. doi: 10.1038/nature22366. Epub 2017 May 17.

12.

Bacterial protein meta-interactomes predict cross-species interactions and protein function.

Caufield JH, Wimble C, Shary S, Wuchty S, Uetz P.

BMC Bioinformatics. 2017 Mar 16;18(1):171. doi: 10.1186/s12859-017-1585-0.

14.

Coevolution is a short-distance force at the protein interaction level and correlates with the modular organization of protein networks.

Liang Z, Xu M, Teng M, Niu L, Wu J.

FEBS Lett. 2010 Oct 8;584(19):4237-40. doi: 10.1016/j.febslet.2010.09.014. Epub 2010 Sep 17.

15.

Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps.

Nabieva E, Jim K, Agarwal A, Chazelle B, Singh M.

Bioinformatics. 2005 Jun;21 Suppl 1:i302-10.

PMID:
15961472
16.

Information flow analysis of interactome networks.

Missiuro PV, Liu K, Zou L, Ross BC, Zhao G, Liu JS, Ge H.

PLoS Comput Biol. 2009 Apr;5(4):e1000350. doi: 10.1371/journal.pcbi.1000350. Epub 2009 Apr 10.

17.

Stratus not altocumulus: a new view of the yeast protein interaction network.

Batada NN, Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hurst LD, Tyers M.

PLoS Biol. 2006 Oct;4(10):e317.

18.

Why do essential proteins tend to be clustered in the yeast interactome network?

Lu C, Hu X, Wang G, Leach LJ, Yang S, Kearsey MJ, Luo ZW.

Mol Biosyst. 2010 May;6(5):871-7. doi: 10.1039/b921069e. Epub 2010 Feb 18.

PMID:
20567773
19.

Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP.

Hawkins T, Chitale M, Kihara D.

BMC Bioinformatics. 2010 May 19;11:265. doi: 10.1186/1471-2105-11-265.

20.

Evolutionary Model Selection and Parameter Estimation for Protein-Protein Interaction Network Based on Differential Evolution Algorithm.

Huang L, Liao L, Wu CH.

IEEE/ACM Trans Comput Biol Bioinform. 2015 May-Jun;12(3):622-31. doi: 10.1109/TCBB.2014.2366748.

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