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How complete are current yeast and human protein-interaction networks?
G Traver Hart, Arun K Ramani, Edward M Marcotte
Genome Biol. 2006; 7(11): 120. Published online 2006 December 1. doi: 10.1186/gb-2006-7-11-120
PMCID:
PMC1794583
Abstract Full Text PDF–185K Supplementary Material
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 Is Cited by the Following 62 Articles in this Archive:
Bayesian Inference for Genomic Data Integration Reduces Misclassification Rate in Predicting Protein-Protein Interactions
Chuanhua Xing, David B. Dunson
PLoS Comput Biol. 2011 July; 7(7): e1002110. Published online 2011 July 28. doi: 10.1371/journal.pcbi.1002110
PMCID:
PMC3145649
Abstract Full Text PDF–543K Supplementary Material
Physical Module Networks: an integrative approach for reconstructing transcription regulation
Noa Novershtern, Aviv Regev, Nir Friedman
Bioinformatics. 2011 July 1; 27(13): i177–i185. Published online 2011 June 14. doi: 10.1093/bioinformatics/btr222
PMCID:
PMC3117354
Abstract Full Text
Modification of Gene Duplicability during the Evolution of Protein Interaction Network
Matteo D'Antonio, Francesca D. Ciccarelli
PLoS Comput Biol. 2011 April; 7(4): e1002029. Published online 2011 April 7. doi: 10.1371/journal.pcbi.1002029
PMCID:
PMC3072358
Abstract Full Text PDF–908K Supplementary Material
Quantitative maps of genetic interactions in yeast - Comparative evaluation and integrative analysis
Rolf O Lindén, Ville-Pekka Eronen, Tero Aittokallio
BMC Syst Biol. 2011; 5: 45. Published online 2011 March 24. doi: 10.1186/1752-0509-5-45
PMCID:
PMC3079637
Abstract Full Text PDF–1.4M Supplementary Material
Understanding protein evolutionary rate by integrating gene co-expression with protein interactions
Kaifang Pang, Chao Cheng, Zhenyu Xuan, Huanye Sheng, Xiaotu Ma
BMC Syst Biol. 2010; 4: 179. Published online 2010 December 30. doi: 10.1186/1752-0509-4-179
PMCID:
PMC3022652
Abstract Full Text PDF–1.7M Supplementary Material
New insights into protein-protein interaction data lead to increased estimates of the S. cerevisiae interactome size
Laure Sambourg, Nicolas Thierry-Mieg
BMC Bioinformatics. 2010; 11: 605. Published online 2010 December 21. doi: 10.1186/1471-2105-11-605
PMCID:
PMC3023808
Abstract Full Text PDF–486K Supplementary Material
Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction
Samira Jaeger, Christine T Sers, Ulf Leser
BMC Genomics. 2010; 11: 717. Published online 2010 December 20. doi: 10.1186/1471-2164-11-717
PMCID:
PMC3017542
Abstract Full Text PDF–1.5M Supplementary Material
DEGAS: De Novo Discovery of Dysregulated Pathways in Human Diseases
Igor Ulitsky, Akshay Krishnamurthy, Richard M. Karp, Ron Shamir
PLoS One. 2010; 5(10): e13367. Published online 2010 October 19. doi: 10.1371/journal.pone.0013367
PMCID:
PMC2957424
Abstract Full Text PDF–1.3M Supplementary Material
Protein Networks Reveal Detection Bias and Species Consistency When Analysed by Information-Theoretic Methods
Luis P. Fernandes, Alessia Annibale, Jens Kleinjung, Anthony C. C. Coolen, Franca Fraternali
PLoS One. 2010; 5(8): e12083. Published online 2010 August 18. doi: 10.1371/journal.pone.0012083
PMCID:
PMC2923596
Abstract Full Text PDF–4.3M Supplementary Material
Inferring modules from human protein interactome classes
Elisabetta Marras, Antonella Travaglione, Gautam Chaurasia, Matthias Futschik, Enrico Capobianco
BMC Syst Biol. 2010; 4: 102. Published online 2010 July 23. doi: 10.1186/1752-0509-4-102
PMCID:
PMC2923113
Abstract Full Text PDF–16M Supplementary Material
Integrative Structure Modeling of Macromolecular Assemblies from Proteomics Data
Keren Lasker, Jeremy L. Phillips, Daniel Russel, Javier Velázquez-Muriel, Dina Schneidman-Duhovny, Elina Tjioe, Ben Webb, Avner Schlessinger, Andrej Sali
Mol Cell Proteomics. 2010 August; 9(8): 1689–1702. Published online 2010 May 27. doi: 10.1074/mcp.R110.000067
PMCID:
PMC2938050
Abstract Full Text Supplementary Material
Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP
Troy Hawkins, Meghana Chitale, Daisuke Kihara
BMC Bioinformatics. 2010; 11: 265. Published online 2010 May 19. doi: 10.1186/1471-2105-11-265
PMCID:
PMC2882935
Abstract Full Text PDF–4.0M
Reconstruction and Validation of RefRec: A Global Model for the Yeast Molecular Interaction Network
Tommi Aho, Henrikki Almusa, Jukka Matilainen, Antti Larjo, Pekka Ruusuvuori, Kaisa-Leena Aho, Thomas Wilhelm, Harri Lähdesmäki, Andreas Beyer, Manu Harju, Sharif Chowdhury, Kalle Leinonen, Christophe Roos, Olli Yli-Harja
PLoS One. 2010; 5(5): e10662. Published online 2010 May 14. doi: 10.1371/journal.pone.0010662
PMCID:
PMC2871048
Abstract Full Text PDF–839K Supplementary Material
Incomplete and noisy network data as a percolation process
Michael P. H. Stumpf, Carsten Wiuf
J R Soc Interface. 2010 October 6; 7(51): 1411–1419. Published online 2010 April 8. doi: 10.1098/rsif.2010.0044
PMCID:
PMC2935600
Abstract Full Text PDF–874K
Building Macromolecular Assemblies by Information-driven Docking: INTRODUCING THE HADDOCK MULTIBODY DOCKING SERVER
Ezgi Karaca, Adrien S. J. Melquiond, Sjoerd J. de Vries, Panagiotis L. Kastritis, Alexandre M. J. J. Bonvin
Mol Cell Proteomics. 2010 August; 9(8): 1784–1794. Published online 2010 March 19. doi: 10.1074/mcp.M000051-MCP201
PMCID:
PMC2938057
Abstract Full Text
Computational approaches for detecting protein complexes from protein interaction networks: a survey
Xiaoli Li, Min Wu, Chee-Keong Kwoh, See-Kiong Ng
BMC Genomics. 2010; 11(Suppl 1): S3. Published online 2010 February 10. doi: 10.1186/1471-2164-11-S1-S3
PMCID:
PMC2822531
Abstract Full Text
Predicting the protein-protein interactions using primary structures with predicted protein surface
Darby Tien-Hao Chang, Yu-Tang Syu, Po-Chang Lin
BMC Bioinformatics. 2010; 11(Suppl 1): S3. Published online 2010 January 18. doi: 10.1186/1471-2105-11-S1-S3
PMCID:
PMC3009501
Abstract Full Text PDF–1.5M
NeMo: Network Module identification in Cytoscape
Corban G Rivera, Rachit Vakil, Joel S Bader
BMC Bioinformatics. 2010; 11(Suppl 1): S61. Published online 2010 January 18. doi: 10.1186/1471-2105-11-S1-S61
PMCID:
PMC3009535
Abstract Full Text PDF–2.2M
Phylogeny-guided interaction mapping in seven eukaryotes
Janusz Dutkowski, Jerzy Tiuryn
BMC Bioinformatics. 2009; 10: 393. Published online 2009 November 30. doi: 10.1186/1471-2105-10-393
PMCID:
PMC2793266
Abstract Full Text PDF–3.3M Supplementary Material
Functionally guided alignment of protein interaction networks for module detection
Waqar Ali, Charlotte M. Deane
Bioinformatics. 2009 December 1; 25(23): 3166–3173. Published online 2009 October 1. doi: 10.1093/bioinformatics/btp569
PMCID:
PMC2778333
Abstract Full Text PDF–524K Supplementary Material
Evolutionarily Conserved Herpesviral Protein Interaction Networks
Even Fossum, Caroline C. Friedel, Seesandra V. Rajagopala, Björn Titz, Armin Baiker, Tina Schmidt, Theo Kraus, Thorsten Stellberger, Christiane Rutenberg, Silpa Suthram, Sourav Bandyopadhyay, Dietlind Rose, Albrecht von Brunn, Mareike Uhlmann, Christine Zeretzke, Yu-An Dong, Hélène Boulet, Manfred Koegl, Susanne M. Bailer, Ulrich Koszinowski, Trey Ideker, Peter Uetz, Ralf Zimmer, Jürgen Haas
PLoS Pathog. 2009 September; 5(9): e1000570. Published online 2009 September 4. doi: 10.1371/journal.ppat.1000570
PMCID:
PMC2731838
Abstract Full Text PDF–1.5M Supplementary Material
Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments
Roberto Mosca, Carles Pons, Juan Fernández-Recio, Patrick Aloy
PLoS Comput Biol. 2009 August; 5(8): e1000490. Published online 2009 August 28. doi: 10.1371/journal.pcbi.1000490
PMCID:
PMC2722787
Abstract Full Text PDF–1.4M Supplementary Material
Assessing the druggability of protein-protein interactions by a supervised machine-learning method
Nobuyoshi Sugaya, Kazuyoshi Ikeda
BMC Bioinformatics. 2009; 10: 263. Published online 2009 August 25. doi: 10.1186/1471-2105-10-263
PMCID:
PMC2739204
Abstract Full Text PDF–721K Supplementary Material
Network-assisted protein identification and data interpretation in shotgun proteomics
Jing Li, Lisa J Zimmerman, Byung-Hoon Park, David L Tabb, Daniel C Liebler, Bing Zhang
Mol Syst Biol. 2009; 5: 303. Published online 2009 August 18. doi: 10.1038/msb.2009.54
PMCID:
PMC2736651
Abstract Full Text PDF–1.3M Supplementary Material
Geometric De-noising of Protein-Protein Interaction Networks
Oleksii Kuchaiev, Marija Rašajski, Desmond J. Higham, Nataša Pržulj
PLoS Comput Biol. 2009 August; 5(8): e1000454. Published online 2009 August 7. doi: 10.1371/journal.pcbi.1000454
PMCID:
PMC2711306
Abstract Full Text PDF–421K Supplementary Material
Ontogeny and phylogeny: molecular signatures of selection, constraint, and temporal pleiotropy in the development of Drosophila
Carlo G Artieri, Wilfried Haerty, Rama S Singh
BMC Biol. 2009; 7: 42. Published online 2009 July 21. doi: 10.1186/1741-7007-7-42
PMCID:
PMC2722573
Abstract Full Text PDF–453K Supplementary Material
Interactome and Gene Ontology provide congruent yet subtly different views of a eukaryotic cell
Antonio Marco, Ignacio Marín
BMC Syst Biol. 2009; 3: 69. Published online 2009 July 15. doi: 10.1186/1752-0509-3-69
PMCID:
PMC2717056
Abstract Full Text PDF–2.3M Supplementary Material
COFECO: composite function annotation enriched by protein complex data
Choong-Hyun Sun, Min-Sung Kim, Youngwoong Han, Gwan-Su Yi
Nucleic Acids Res. 2009 July 1; 37(Web Server issue): W350–W355. Published online 2009 July 1. doi: 10.1093/nar/gkp331
PMCID:
PMC2703949
Abstract Full Text PDF–3.5M Supplementary Material
Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression
Stefanie De Bodt, Sebastian Proost, Klaas Vandepoele, Pierre Rouzé, Yves Van de Peer
BMC Genomics. 2009; 10: 288. Published online 2009 June 29. doi: 10.1186/1471-2164-10-288
PMCID:
PMC2719670
Abstract Full Text PDF–1.2M Supplementary Material
Triangle network motifs predict complexes by complementing high-error interactomes with structural information
Bill Andreopoulos, Christof Winter, Dirk Labudde, Michael Schroeder
BMC Bioinformatics. 2009; 10: 196. Published online 2009 June 27. doi: 10.1186/1471-2105-10-196
PMCID:
PMC2714575
Abstract Full Text PDF–3.0M Supplementary Material
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