Improving protein complex prediction by reconstructing a high-confidence protein-protein interaction network of Escherichia coli from different physical interaction data sources

[1]  Peter Uetz,et al.  Protein-protein Interaction Networks of E. coli and S. cerevisiae are similar , 2014, Scientific Reports.

[2]  Marco Y. Hein,et al.  Accurate Protein Complex Retrieval by Affinity Enrichment Mass Spectrometry (AE-MS) Rather than Affinity Purification Mass Spectrometry (AP-MS)* , 2014, Molecular & Cellular Proteomics.

[3]  Qianghu Wang,et al.  Integration Strategy Is a Key Step in Network-Based Analysis and Dramatically Affects Network Topological Properties and Inferring Outcomes , 2014, BioMed research international.

[4]  Clara Pizzuti,et al.  Algorithms and tools for protein-protein interaction networks clustering, with a special focus on population-based stochastic methods , 2014, Bioinform..

[5]  Debora S. Marks,et al.  Sequence co-evolution gives 3D contacts and structures of protein complexes , 2014, bioRxiv.

[6]  Fang-Xiang Wu,et al.  Identifying protein complexes and functional modules - from static PPI networks to dynamic PPI networks , 2014, Briefings Bioinform..

[7]  P. Uetz,et al.  The binary protein-protein interaction landscape of Escherichia coli , 2014, Nature Biotechnology.

[8]  Zhu-Hong You,et al.  Prediction of protein-protein interactions from amino acid sequences with ensemble extreme learning machines and principal component analysis , 2013, BMC Bioinformatics.

[9]  N. Perrimon,et al.  Protein Complex–Based Analysis Framework for High-Throughput Data Sets , 2013, Science Signaling.

[10]  Shira L. Broschat,et al.  Using Protein Clusters from Whole Proteomes to Construct and Augment a Dendrogram , 2013, Adv. Bioinformatics.

[11]  D. Baker,et al.  Structural and energetic basis of folded protein transport by the FimD usher , 2013, Nature.

[12]  Xue-wen Chen,et al.  Heterogeneous data integration by tree‐augmented naïve Bayes for protein–protein interactions prediction , 2013, Proteomics.

[13]  Edson L. Folador,et al.  Computational Prediction of Protein-Protein Interactions in Leishmania Predicted Proteomes , 2012, PloS one.

[14]  Bonnie Berger,et al.  A computational framework for boosting confidence in high-throughput protein-protein interaction datasets , 2012, Genome Biology.

[15]  B. Honig,et al.  Structure-based prediction of protein-protein interactions on a genome-wide scale , 2012, Nature.

[16]  Haiyuan Yu,et al.  Detecting overlapping protein complexes in protein-protein interaction networks , 2012, Nature Methods.

[17]  Lars Malmström,et al.  The Proteome Folding Project: proteome-scale prediction of structure and function. , 2011, Genome research.

[18]  B. De Moor,et al.  COMODO: an adaptive coclustering strategy to identify conserved coexpression modules between organisms , 2010, Nucleic acids research.

[19]  Yunlong Liu,et al.  2K09 and thereafter : the coming era of integrative bioinformatics, systems biology and intelligent computing for functional genomics and personalized medicine research , 2010, BMC Genomics.

[20]  Gary D. Bader,et al.  Cytoscape Web: an interactive web-based network browser , 2010, Bioinform..

[21]  P. Bork,et al.  Proteome Organization in a Genome-Reduced Bacterium , 2009, Science.

[22]  Chong Su,et al.  The Modular Organization of Protein Interactions in Escherichia coli , 2009, PLoS Comput. Biol..

[23]  S. Gygi,et al.  Defining the Human Deubiquitinating Enzyme Interaction Landscape , 2009, Cell.

[24]  A. Emili,et al.  Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins , 2009, PLoS biology.

[25]  J. Collado-Vides,et al.  DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli , 2009, Genome Biology.

[26]  Peter D. Karp,et al.  EcoCyc: A comprehensive view of Escherichia coli biology , 2008, Nucleic Acids Res..

[27]  Andrea Lancichinetti,et al.  Detecting the overlapping and hierarchical community structure in complex networks , 2008, 0802.1218.

[28]  S. Kanaya,et al.  Large-scale identification of protein-protein interaction of Escherichia coli K-12. , 2006, Genome research.

[29]  K. Lee,et al.  A new meta-heuristic algorithm for continuous engineering optimization: harmony search theory and practice , 2005 .

[30]  Leon Danon,et al.  Comparing community structure identification , 2005, cond-mat/0505245.

[31]  A. Emili,et al.  Interaction network containing conserved and essential protein complexes in Escherichia coli , 2005, Nature.

[32]  Ian M. Donaldson,et al.  BIND: the Biomolecular Interaction Network Database , 2001, Nucleic Acids Res..

[33]  S. Dongen.  Graph clustering by flow simulation , 2000 .

[34]  T. Vicsek,et al.  Data and text mining CFinder : locating cliques and overlapping modules in biological networks , 2006 .

[35]  Martin Vingron,et al.  IntAct: an open source molecular interaction database , 2004, Nucleic Acids Res..

[36]  Ioannis Xenarios,et al.  DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions , 2002, Nucleic Acids Res..

[37]  Yi Pan,et al.  Identifying protein complexes from interaction networks based on clique percolation and distance restriction , 2010, BMC Genomics.