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Comparative network-based recovery analysis and proteomic profiling of neurological changes in valproic acid-treated mice.

Goh WW, Sergot MJ, Sng JC, Wong L.

J Proteome Res. 2013 May 3;12(5):2116-27. doi: 10.1021/pr301127f. Epub 2013 Apr 17. Erratum in: J Proteome Res. 2013 Oct 4;12(10):4650. Sng, Judy Cg [corrected to Sng, Judy C G].


Functional module search in protein networks based on semantic similarity improves the analysis of proteomics data.

Boyanova D, Nilla S, Klau GW, Dandekar T, Müller T, Dittrich M.

Mol Cell Proteomics. 2014 Jul;13(7):1877-89. doi: 10.1074/mcp.M113.032839. Epub 2014 May 7.


Evaluation of clustering algorithms for protein complex and protein interaction network assembly.

Sardiu ME, Florens L, Washburn MP.

J Proteome Res. 2009 Jun;8(6):2944-52. doi: 10.1021/pr900073d.


Proteomics signature profiling (PSP): a novel contextualization approach for cancer proteomics.

Goh WW, Lee YH, Ramdzan ZM, Sergot MJ, Chung M, Wong L.

J Proteome Res. 2012 Mar 2;11(3):1571-81. doi: 10.1021/pr200698c. Epub 2012 Feb 9.


Gene network and proteomic analyses of cardiac responses to pathological and physiological stress.

Drozdov I, Didangelos A, Yin X, Zampetaki A, Abonnenc M, Murdoch C, Zhang M, Ouzounis CA, Mayr M, Tsoka S, Shah AM.

Circ Cardiovasc Genet. 2013 Dec;6(6):588-97. doi: 10.1161/CIRCGENETICS.113.000063. Epub 2013 Nov 8.


The bait compatibility index: computational bait selection for interaction proteomics experiments.

Saha S, Kaur P, Ewing RM.

J Proteome Res. 2010 Oct 1;9(10):4972-81. doi: 10.1021/pr100267t.


Construction of protein interaction networks based on the label-free quantitative proteomics.

Sardiu ME, Washburn MP.

Methods Mol Biol. 2011;781:71-85. doi: 10.1007/978-1-61779-276-2_5.


Categorizing biases in high-confidence high-throughput protein-protein interaction data sets.

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

Mol Cell Proteomics. 2011 Dec;10(12):M111.012500. doi: 10.1074/mcp.M111.012500. Epub 2011 Aug 29.


Proteomic and bioinformatic analysis of membrane proteome in type 2 diabetic mouse liver.

Kim GH, Park EC, Yun SH, Hong Y, Lee DG, Shin EY, Jung J, Kim YH, Lee KB, Jang IS, Lee ZW, Chung YH, Choi JS, Cheong C, Kim S, Kim SI.

Proteomics. 2013 Apr;13(7):1164-79. doi: 10.1002/pmic.201200210. Epub 2013 Feb 26.


New data analysis and mining approaches identify unique proteome and transcriptome markers of susceptibility to autoimmune diabetes.

Gerling IC, Singh S, Lenchik NI, Marshall DR, Wu J.

Mol Cell Proteomics. 2006 Feb;5(2):293-305. Epub 2005 Oct 16.


Proteomic analysis of rat prefrontal cortex after chronic valproate treatment.

Thangavel M, Seelan RS, Lakshmanan J, Vadnal RE, Stagner JI, Parthasarathy LK, Casanova MF, El-Mallakh RS, Parthasarathy RN.

J Neurosci Res. 2014 Jul;92(7):927-36. doi: 10.1002/jnr.23373. Epub 2014 Apr 1.


Proteomic profiling of bronchoalveolar lavage fluid in critically ill patients with ventilator-associated pneumonia.

Nguyen EV, Gharib SA, Palazzo SJ, Chow YH, Goodlett DR, Schnapp LM.

PLoS One. 2013;8(3):e58782. doi: 10.1371/journal.pone.0058782. Epub 2013 Mar 7.


Triangle network motifs predict complexes by complementing high-error interactomes with structural information.

Andreopoulos B, Winter C, Labudde D, Schroeder M.

BMC Bioinformatics. 2009 Jun 27;10:196. doi: 10.1186/1471-2105-10-196.


Utilizing both topological and attribute information for protein complex identification in PPI networks.

Hu AL, Chan KC.

IEEE/ACM Trans Comput Biol Bioinform. 2013 May-Jun;10(3):780-92. doi: 10.1109/TCBB.2013.37.


Development and implementation of an algorithm for detection of protein complexes in large interaction networks.

Altaf-Ul-Amin M, Shinbo Y, Mihara K, Kurokawa K, Kanaya S.

BMC Bioinformatics. 2006 Apr 14;7:207.


Computational framework for analysis of prey-prey associations in interaction proteomics identifies novel human protein-protein interactions and networks.

Saha S, Dazard JE, Xu H, Ewing RM.

J Proteome Res. 2012 Sep 7;11(9):4476-87. doi: 10.1021/pr300227y. Epub 2012 Aug 21.


Construction of ontology augmented networks for protein complex prediction.

Zhang Y, Lin H, Yang Z, Wang J.

PLoS One. 2013 May 1;8(5):e62077. doi: 10.1371/journal.pone.0062077. Print 2013.


Mapping the protein interaction network of the human COP9 signalosome complex using a label-free QTAX strategy.

Fang L, Kaake RM, Patel VR, Yang Y, Baldi P, Huang L.

Mol Cell Proteomics. 2012 May;11(5):138-47. doi: 10.1074/mcp.M111.016352. Epub 2012 Apr 3.


Antennal proteome comparison of sexually mature drone and forager honeybees.

Feng M, Song F, Aleku DW, Han B, Fang Y, Li J.

J Proteome Res. 2011 Jul 1;10(7):3246-60. doi: 10.1021/pr2002808. Epub 2011 Jun 13.

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