Protein–Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks

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[1]  Benjamin A. Shoemaker,et al.  Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners , 2007, PLoS Comput. Biol..

[2]  Rafael C. Jimenez,et al.  The IntAct molecular interaction database in 2012 , 2011, Nucleic Acids Res..

[3]  Maria Victoria Schneider,et al.  MINT: a Molecular INTeraction database. , 2002, FEBS letters.

[4]  Benjamin A. Shoemaker,et al.  Deciphering Protein–Protein Interactions. Part I. Experimental Techniques and Databases , 2007, PLoS Comput. Biol..

[5]  Carlos Prieto,et al.  APID2NET: unified interactome graphic analyzer , 2007, Bioinform..

[6]  Thomas Schlitt,et al.  Protein-protein interaction databases: keeping up with growing interactomes , 2009, Human Genomics.

[7]  C. Prieto,et al.  Structural domain–domain interactions: Assessment and comparison with protein–protein interaction data to improve the interactome , 2010, Proteins.

[8]  Baris E. Suzek,et al.  The Universal Protein Resource (UniProt) in 2010 , 2009, Nucleic Acids Res..

[9]  Jianmin Wu,et al.  Integrated network analysis platform for protein-protein interactions , 2009, Nature Methods.

[10]  Peter Woollard,et al.  The minimum information required for reporting a molecular interaction experiment (MIMIx) , 2007, Nature Biotechnology.

[11]  Adam J. Smith,et al.  The Database of Interacting Proteins: 2004 update , 2004, Nucleic Acids Res..

[12]  Peter B. McGarvey,et al.  Infrastructure for the life sciences: design and implementation of the UniProt website , 2009, BMC Bioinformatics.

[13]  John Boyle,et al.  Cytoscape: a community-based framework for network modeling. , 2009, Methods in molecular biology.

[14]  Susumu Goto,et al.  KEGG for representation and analysis of molecular networks involving diseases and drugs , 2009, Nucleic Acids Res..

[15]  Igor Stagljar,et al.  Two-hybrid technologies in proteomics research. , 2008, Current opinion in biotechnology.

[16]  Carlos Prieto,et al.  Human Gene Coexpression Landscape: Confident Network Derived from Tissue Transcriptomic Profiles , 2008, PloS one.

[17]  A. Grigoriev On the number of protein-protein interactions in the yeast proteome. , 2003, Nucleic acids research.

[18]  Christian von Mering,et al.  STRING 8—a global view on proteins and their functional interactions in 630 organisms , 2008, Nucleic Acids Res..

[19]  A. Barabasi,et al.  High-Quality Binary Protein Interaction Map of the Yeast Interactome Network , 2008, Science.

[20]  Carlos Prieto,et al.  APID: Agile Protein Interaction DataAnalyzer , 2006, Nucleic Acids Res..

[21]  Nathan Blow,et al.  Systems biology: Untangling the protein web , 2009, Nature.

[22]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[23]  Robert P. St.Onge,et al.  Defining genetic interaction , 2008, Proceedings of the National Academy of Sciences.

[24]  M. Vidal,et al.  Interactome: gateway into systems biology. , 2005, Human molecular genetics.

[25]  Luana Licata,et al.  Protein interactions: integration leads to belief. , 2008, Trends in biochemical sciences.

[26]  Jing Gao,et al.  Integrating and annotating the interactome using the MiMI plugin for cytoscape , 2009, Bioinform..

[27]  Merlin Crossley,et al.  Protein interactions: is seeing believing? , 2007, Trends in biochemical sciences.

[28]  M. Vidal,et al.  Literature-curated protein interaction datasets , 2009, Nature Methods.

[29]  Michael S. Livstone,et al.  Recurated protein interaction datasets , 2009, Nature Methods.

[30]  Ben Lehner,et al.  Tissue specificity and the human protein interaction network , 2009, Molecular systems biology.

[31]  Livia Perfetto,et al.  MINT, the molecular interaction database: 2012 update , 2011, Nucleic Acids Res..

[32]  Peer Bork,et al.  KEGG Atlas mapping for global analysis of metabolic pathways , 2008, Nucleic Acids Res..

[33]  Sara Linse,et al.  Methods for the detection and analysis of protein–protein interactions , 2007, Proteomics.

[34]  David L. Robertson,et al.  Protein Interactions from Complexes: A Structural Perspective , 2006, Comparative and functional genomics.

[35]  Kara Dolinski,et al.  The BioGRID Interaction Database: 2008 update , 2008, Nucleic Acids Res..