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Protein-protein interaction networks and biology—what's the connection?
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“Notably, edges are susceptible to ascertainment biases52,214,215 and confounding factors that can induce spurious relationships178 (FIG. 2b).”
From Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders (2015) · cites this paper as [52]
Citations
Cites
Emergence of Scaling in Random Networks
Barabási, A.-L., & Albert, R. (1999) · Science · doi:10.1126/science.286.5439.509 · Cited by 36,135
Network biology: understanding the cell's functional organization
Barabási, A.-L., & Oltvai, Z. N. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1272 · Cited by 7,903
Error and attack tolerance of complex networks
Albert, R., Jeong, H., & Barabási, A.-L. (2000) · Nature · doi:10.1038/35019019 · Cited by 7,534
Error and attack tolerance of complex networksPreprint
Albert, R., Jeong, H., & Barabási, A.-Ĺ. (2000) · Cited by 6,554
Lethality and centrality in protein networks
Jeong, H., Mason, S., Barabási, A., & Oltvai, Z. (2001) · Nature · doi:10.1038/35075138 · Cited by 5,327
A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae
Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., et al. (2000) · Nature · doi:10.1038/35001009 · Cited by 4,706
A comprehensive two-hybrid analysis to explore the yeast protein interactome
Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., & Sakaki, Y. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.061034498 · Cited by 3,566
Specificity and Stability in Topology of Protein Networks
Maslov, S., & Sneppen, K. (2002) · Science · doi:10.1126/science.1065103 · Cited by 3,051
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
Krogan, N. J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A., et al. (2006) · Nature · doi:10.1038/nature04670 · Cited by 2,969
Proteome survey reveals modularity of the yeast cell machinery
Gavin, A., Aloy, P., Grandi, P., Krause, R., Böesche, M., Marzioch, M., Rau, C., Jensen, L. J., Bastuck, S., Dümpelfeld, B., et al. (2006) · Nature · doi:10.1038/nature04532 · Cited by 2,570
Comparative assessment of large-scale data sets of protein–protein interactions
von Mering, C., Krause, R., Snel, ., Cornell, M. J., Oliver, S. G., Fields, S., & Peer Bork, B. (2002) · Nature · doi:10.1038/nature750 · Cited by 2,339
Evidence for dynamically organized modularity in the yeast protein–protein interaction network
Han, J. J., Bertin, N., Hao, T., Goldberg, D. S., Berriz, G. F., Zhang, L. V., Dupuy, D., Walhout, A. J. M., Cusick, M. E., Roth, F. P., et al. (2004) · Nature · doi:10.1038/nature02555 · Cited by 1,789
Subnets of scale-free networks are not scale-free: Sampling properties of networks
Stumpf, M. P. H., Wiuf, C., & May, R. M. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0501179102 · Cited by 562
Brandes, U., & Erlebach, T. (2005) · Lecture notes in computer science · doi:10.1007/b106453 · Cited by 512
Functional topology in a network of protein interactions
Pržulj, N., Wigle, D. A., & Jurišica, I. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg415 · Cited by 415
How complete are current yeast and human protein-interaction networks?
Hart, T., Ramani, A. K., & Marcotte, E. M. (2006) · Genome biology · doi:10.1186/gb-2006-7-11-120 · Cited by 407
Classification of scale-free networks
Goh, K.-I., Oh, E., Jeong, H., Kahng, B., & Kim, D. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202301299 · Cited by 378
Ekman, D. S., Light, S., Björklund, Å. K., & Elofsson, A. (2006) · Genome biology · doi:10.1186/gb-2006-7-6-r45 · Cited by 378
Effect of sampling on topology predictions of protein-protein interaction networks
Han, J. J., Dupuy, D., Bertin, N., Cusick, M. E., & Vidal, M. (2005) · Nature Biotechnology · doi:10.1038/nbt1116 · Cited by 336
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
Reguly, T., Breitkreutz, A., Boucher, L., Breitkreutz, B.-J., Hon, G. C., Myers, C. L., Parsons, A., Friesen, H., Oughtred, R., Tong, A., et al. (2006) · Journal of Biology · doi:10.1186/jbiol36 · Cited by 326
Evolutionary and Physiological Importance of Hub Proteins
Batada, N. N., Hurst, L. D., & Tyers, M. (2005) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020088 · Cited by 284
Adai, A. T., Date, S. V., Wieland, S. C., & Marcotte, E. M. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.04.047 · Cited by 223
Stratus Not Altocumulus: A New View of the Yeast Protein Interaction Network
Batada, N. N., Reguly, T., Breitkreutz, A., Boucher, L., Breitkreutz, B., Hurst, L. D., & Tyers, M. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040317 · Cited by 218
Berg, J., Lässig, M., & Wagner, A. (2004) · BMC Evolutionary Biology · doi:10.1186/1471-2148-4-51 · Cited by 205
Duplication-divergence model of protein interaction network
Ispolatov, Y., Krapivsky, P. L., & Yuryev, A. (2005) · Physical Review E · doi:10.1103/physreve.71.061911 · Cited by 180
A direct comparison of protein interaction confidence assignment schemes
Suthram, S., Shlomi, T., Ruppin, E., Sharan, R., & Ideker, T. E. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-360 · Cited by 117
Still Stratus Not Altocumulus: Further Evidence against the Date/Party Hub Distinction
Batada, N. N., Reguly, T., Breitkreutz, A., Boucher, L., Breitkreutz, B., Hurst, L. D., & Tyers, M. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050154 · Cited by 113
Sampling properties of random graphs: The degree distribution
Stumpf, M. P. H., & Wiuf, C. (2005) · Physical Review E · doi:10.1103/physreve.72.036118 · Cited by 109
Xia, K., Xue, H., Dong, D., Zhu, S., Wang, J., Zhang, Q., Hou, L., Chen, H., Tao, R., Huang, Z., et al. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020145 · Cited by 100
Confirmation of Organized Modularity in the Yeast Interactome
Bertin, N., Simonis, N., Dupuy, D., Cusick, M. E., Han, J. J., Fraser, H. B., Roth, F. P., & Vidal, M. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050153 · Cited by 100
Potential artefacts in protein‐interaction networks
Aloy, P., & Russell, R. B. (2002) · FEBS Letters · doi:10.1016/s0014-5793(02)03427-0 · Cited by 70
The effects of incomplete protein interaction data on structural and evolutionary inferences
de Silva, E., Thorne, T., Ingram, P. J., Agrafioti, I., Swire, J. S., Wiuf, C., & Stumpf, M. P. H. (2006) · BMC Biology · doi:10.1186/1741-7007-4-39 · Cited by 67
An Exponential Core in the Heart of the Yeast Protein Interaction Network
Pereira‐Leal, J. B., Audit, B., Peregrín-Alvarez, J. M., & Ouzounis, C. A. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msi024 · Cited by 59
The evolution of network topology by selective removal
Salathé, M., May, R. M., & Bonhoeffer, S. (2005) · Journal of The Royal Society Interface · doi:10.1098/rsif.2005.0072 · Cited by 33
Effect of dataset selection on the topological interpretation of protein interaction networks
Hakes, L., Robertson, D. L., & Oliver, S. G. (2005) · BMC Genomics · doi:10.1186/1471-2164-6-131 · Cited by 22
Self-citationGrowing biological networks: Beyond the gene-duplication model
Bersini, H., Lenaerts, T., & Santos, F. C. (2006) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2005.12.012 · Cited by 16
Cited by
Sorted by citations
Uncovering disease-disease relationships through the incomplete interactome
Menche, J., Sharma, A., Kitsak, M., Ghiassian, S. D., Vidal, M., Loscalzo, J., & Barabási, A.-L. (2015) · Science · doi:10.1126/science.1257601 · Cited by 1,546
“Despite the best curation efforts, both the in-teractome and the disease gene list remain incomplete( 6 , 11 – 16 )andbiasedtowardmuch-studied disease genes and disease mechanisms ( 32 , 33 ).”
Structure and dynamics of molecular networks: A novel paradigm of drug discovery
Csermely, P., Korcsmáros, T., Kiss, H., London, G., & Nussinov, R. (2013) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2013.01.016 · Cited by 911
“Since different methods have different biases, composite scores taking multiple data-types into account perform better (Hakes et al., 2008; Sanchez Claros & Tramontano, 2012).”
BackgroundMethodSystems biology and gene networks in neurodevelopmental and neurodegenerative disorders
Parikshak, N. N., Gandal, M. J., & Geschwind, D. H. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3934 · Cited by 430
“The genome-wide approaches yield many more interactions, so most databases typically combine both target-focused and genome-wide experiments 52 .”
BackgroundLi, S., Zhang, B., & Zhang, N. (2011) · BMC Systems Biology · doi:10.1186/1752-0509-5-s1-s10 · Cited by 381
“Moreover, NIMS is also relatively robust to the background network, although available networks such as the PPI network are still incomplete and biased (Figure 3c) [54].”
BackgroundPredicting Protein–Protein Interactions from the Molecular to the Proteome Level
Keskin, O., Tuncbag, N., & Gursoy, A. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00683 · Cited by 369
Metadata
- Authors
- Hakes, L., Pinney, J. W., Robertson, D. L., & Lovell, S. C.
- Affiliations
- University of Manchester (GB)
- Venue
- Nature Biotechnology
- Published
- 2008-01
- Volume
- 26
- Issue
- 1
- Pages
- 69-72
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2165160727
- Cited by
- 200
- References
- 37
- Citations by year
- 2026: 2 · 2025: 9 · 2024: 7 · 2023: 12 · 2022: 5 · 2021: 3 · 2020: 3 · 2019: 4 · 2018: 9 · 2017: 15 · 2016: 13 · 2015: 17 · 2014: 10 · 2013: 17 · 2012: 16
- FWCI
- 7.96
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- Research Explorer (The University of Manchester) (publishedVersion)
- ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (submittedVersion)
- Funders
- Wellcome Trust
- Biotechnology and Biological Sciences Research Council (BB/F007620/1, BB/C515412/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- protein-protein interaction network, network analysis
- MeSH terms
- Algorithms, Binding Sites, Biology, Protein Binding, Sensitivity and Specificity, Signal Transduction, Information Storage and Retrieval, Artifacts, Proteome, Protein Interaction Mapping
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