Article

Global alignment of protein-protein interaction networks.

Computer Science Department, University of California Santa Barbara, Santa Barbara, CA, USA.
Methods in molecular biology (Clifton, N.J.) (Impact Factor: 1.29). 01/2013; 939:21-34. DOI: 10.1007/978-1-62703-107-3_3
Source: PubMed

ABSTRACT Sequence-based comparisons have been the workhorse of bioinformatics for the past four decades, furthering our understanding of gene function and evolution. Over the last decade, a plethora of technologies have matured for measuring Protein-protein interactions (PPIs) at large scale, yielding comprehensive PPI networks for over ten species. In this chapter, we review methods for harnessing PPI networks to improve the detection of orthologous proteins across species. In particular, we focus on pairwise global network alignment methods that aim to find a mapping between the networks of two species that maximizes the sequence and interaction similarities between matched nodes. We further suggest a novel evolutionary-based global alignment algorithm. We then compare the different methods on a yeast-fly-worm benchmark, discuss their performance differences, and conclude with open directions for future research.

1 Bookmark
 · 
129 Views
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Phytonematodes use a stylet and secreted effectors to modify host cells and ingest nutrients to support their growth and development. The molecular function of nematode effectors is currently the subject of intense investigation. In this review, we summarize our current understanding of nematode effectors, with a particular focus on proteinaceous stylet-secreted effectors of sedentary endoparasitic phytonematodes, for which a wealth of information has surfaced in the past 10 yr. We provide an update on the effector repertoires of several of the most economically important genera of phytonematodes and discuss current approaches to dissecting their function. Lastly, we highlight the latest breakthroughs in effector discovery that promise to shed new light on effector diversity and function across the phylum Nematoda.
    New Phytologist 05/2013; DOI:10.1111/nph.12323 · 6.55 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: We present here a compact overview of the data, models and methods proposed for the analysis of biological networks based on the search for significant repetitions. In particular, we concentrate on three problems widely studied in the literature: 'network alignment', 'network querying' and 'network motif extraction'. We provide (i) details of the experimental techniques used to obtain the main types of interaction data, (ii) descriptions of the models and approaches introduced to solve such problems and (iii) pointers to both the available databases and software tools. The intent is to lay out a useful roadmap for identifying suitable strategies to analyse cellular data, possibly based on the joint use of different interaction data types or analysis techniques.
    Briefings in Bioinformatics 12/2013; 16(1). DOI:10.1093/bib/bbt084 · 5.30 Impact Factor

Full-text

Download
159 Downloads
Available from
May 21, 2014