The DOI matches its Crossref record; 46 of the 46 references it cites were found in a registry or an index.
High-Quality Binary Protein Interaction Map of the Yeast Interactome Network
Open accessAbstract
Current yeast interactome network maps contain several hundred molecular complexes with limited and somewhat controversial representation of direct binary interactions. We carried out a comparative quality assessment of current yeast interactome data sets, demonstrating that high-throughput yeast two-hybrid (Y2H) screening provides high-quality binary interaction information. Because a large fraction of the yeast binary interactome remains to be mapped, we developed an empirically controlled mapping framework to produce a “second-generation” high-quality, high-throughput Y2H data set covering ∼20% of all yeast binary interactions. Both Y2H and affinity purification followed by mass spectrometry (AP/MS) data are of equally high quality but of a fundamentally different and complementary nature, resulting in networks with different topological and biological properties. Compared to co-complex interactome models, this binary map is enriched for transient signaling interactions and intercomplex connections with a highly significant clustering between essential proteins. Rather than correlating with essentiality, protein connectivity correlates with genetic pleiotropy.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Several high-throughput experimental techniques have been designed to identify interacting protein partners23–26, but their results are far from complete and are often mutually inconsistent.”
From AF2Complex predicts direct physical interactions in multimeric proteins with deep learning (2022) · cites this paper as [26]
In the citing paper
“Yeast two hybrid (Y2H), affinity-purification mass spectrometry (APMS), and other high-throughput experimental approaches have identified many pairs of interacting proteins in yeast and other organisms (1–5), but there are discrepancies between sets generated using the different methods and considerable false positive and false negative rates (6–8).”
From Computed structures of core eukaryotic protein complexes (2021) · cites this paper as [5]
In the citing paper
“In a first set of calculations, we found that even with the advantages of S. cerevisiae and improved ortholog identification, the statistical method (Direct Coupling Analysis, DCA) we had used in our previous coevolution-guided protein-protein interaction (PPI) screen in Prokaryotes (9) (the more accurate GREMLIN (11) method is too slow for this) could not effectively distinguish a “gold standard””
From Computed structures of core eukaryotic protein complexes (2021) · cites this paper as [5]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
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 motifs: simple building blocks of complex networks.
Milo, R., Shen-Orr, S., Itzkovitz, S., Kashtan, N., Chklovskii, D., & Alon, U. (2002) · Science · doi:10.1126/science.298.5594.824 · Cited by 7,368
Lethality and centrality in protein networks
Jeong, H., Mason, S., Barabási, A., & Oltvai, Z. (2001) · Nature · doi:10.1038/35075138 · Cited by 5,327
Functional organization of the yeast proteome by systematic analysis of protein complexes
Gavin, A., Böesche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A., Cruciat, C., et al. (2002) · Nature · doi:10.1038/415141a · Cited by 4,729
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
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
Ho, Y., Gruhler, A., Heilbut, A. M., Bader, G. D., Moore, L., Adams, S., Millar, A., Taylor, P. P., Bennett, K. L., Boutilier, K., et al. (2002) · Nature · doi:10.1038/415180a · Cited by 3,573
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
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 2,964
Self-citationTranscriptional Regulatory Networks in Saccharomyces cerevisiae
Lee, T. I., Rinaldi, N. J., Robert, F., Odom, D. T., Bar-Joseph, Z., Gerber, G. K., Hannett, N. M., Harbison, C. T., Thompson, C. M., Simon, I., et al. (2002) · Science · doi:10.1126/science.1075090 · Cited by 2,956
Towards a proteome-scale map of the human protein–protein interaction network
Rual, J.-F. M., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., Berriz, G. F., Gibbons, F. D., Dreze, M., Ayivi-Guedehoussou, N., et al. (2005) · Nature · doi:10.1038/nature04209 · Cited by 2,904
Self-citation
Flagged first, then by citations
Research works printed but not linked: 2
- I. Remy, S. W. Michnick, Methods Mol. Biol.261, 411 (2004).
- A. M. Dudley, D. M. Janse, A. Tanay, R. Shamir, G. M. Church, Mol. Syst. Biol.1, 0001 (2005).
Cited by
Sorted by citations
Items 201–300 of 1,000
Constructing minimal models for complex system dynamics
Barzel, B., Liu, Y., & Barabási, A.-Ĺ. (2015) · Nature Communications · doi:10.1038/ncomms8186 · Cited by 103
Reimand, J., Vaquerizas, J. M., Todd, A. E., Vilo, J., & Luscombe, N. M. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq232 · Cited by 102
Yeast two-hybrid methods and their applications in drug discovery
Hamdi, A., & Colas, P. (2011) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2011.10.008 · Cited by 103
Protein–protein interaction networks and subnetworks in the biology of disease
Nibbe, R. K., Chowdhury, S. A., Koyutürk, M., Ewing, R. M., & Chance, M. R. (2010) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.121 · Cited by 101
Hub Protein Controversy: Taking a Closer Look at Plant Stress Response Hubs
Vandereyken, K., Leene, J. V., Coninck, B. D., & Cammue, B. P. A. (2018) · Frontiers in Plant Science · doi:10.3389/fpls.2018.00694 · Cited by 99
Li, M., Zheng, R., Zhang, H., Wang, J., & Pan, Y. F. (2014) · Methods · doi:10.1016/j.ymeth.2014.02.016 · Cited by 99
Determinants and Regulation of Protein Turnover in Yeast
Martin-Perez, M., & Villén, J. (2017) · Cell Systems · doi:10.1016/j.cels.2017.08.008 · Cited by 99
Targeting and tinkering with interaction networks
Russell, R. B., & Aloy, P. (2008) · Nature Chemical Biology · doi:10.1038/nchembio.119 · Cited by 99
The function of communities in protein interaction networks at multiple scales
Lewis, A. C. F., Jones, N. S., Porter, M. A., & Deane, C. M. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-100 · Cited by 100
Systems Analysis of Plant Functional, Transcriptional, Physical Interaction, and Metabolic Networks
Bassel, G. W., Gaudinier, A., Brady, S. M., Hennig, L., Rhee, S. Y., & Smet, I. D. (2012) · The Plant Cell · doi:10.1105/tpc.112.100776 · Cited by 101
A Consensus of Core Protein Complex Compositions for Saccharomyces cerevisiae
Benschop, J. J., Brabers, N., van Leenen, D., Bakker, L. V., van Deutekom, H. W. M., van Berkum, N. L., Apweiler, E., Lijnzaad, P., Holstege, F. C. P., & Kemmeren, P. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.06.002 · Cited by 96
Exploiting Amino Acid Composition for Predicting Protein-Protein Interactions
Roy, S., Martinez, D., Platero, H., Lane, T. D. R., & Werner‐Washburne, M. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007813 · Cited by 96
Yuga, M., Gomi, K., Klionsky, D. J., & Shintani, T. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.173906 · Cited by 98
Tran, H., Nimick, M., Uhrig, R. G., Templeton, G. W., MORRICE, N. A., Gourlay, R., DeLong, A., & Moorhead, G. B. G. (2012) · The Plant Journal · doi:10.1111/j.1365-313x.2012.04984.x · Cited by 95
The eisosome core is composed of BAR domain proteins
Olivera-Couto, A., Graña, M., Harispe, L., & Aguilar, P. S. (2011) · Molecular Biology of the Cell · doi:10.1091/mbc.e10-12-1021 · Cited by 98
Global Protein−Protein Interaction Network in the Human Pathogen Mycobacterium tuberculosis H37Rv
Wang, Y., Cui, T., Zhang, C., Yang, M., Huang, Y., Li, W., Zhang, L., Gao, C., He, Y., Li, Y., et al. (2010) · Journal of Proteome Research · doi:10.1021/pr100808n · Cited by 94
Kevei, Z., Baloban, M., Ines, O. D., Tiricz, H., Kröll, A., Regulski, K., Mergaert, P., & Kondorosi, É. (2011) · PLoS ONE · doi:10.1371/journal.pone.0020618 · Cited by 96
Understanding Modularity in Molecular Networks Requires Dynamics
Alexander, R. P., Kim, P. M., Emonet, T., & Gerstein, M. (2009) · Science Signaling · doi:10.1126/scisignal.281pe44 · Cited by 94
Compartmentalization and transporter engineering strategies for terpenoid synthesis
Jin, K., Xia, H., Liu, Y., Li, J., Du, G., Lv, X., & Liu, L. (2022) · Microbial Cell Factories · doi:10.1186/s12934-022-01819-z · Cited by 92
Crystal Structure of Get4-Get5 Complex and Its Interactions with Sgt2, Get3, and Ydj1
Chang, Y., Chuang, Y.-C., Ho, Y.-C., Cheng, M.-Y., Sun, Y., Hsiao, C., & Wang, C. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.087098 · Cited by 92
Ugo1 and Mdm30 act sequentially during Fzo1-mediated mitochondrial outer membrane fusion
den Brave, F., Fres, J. M., Schauss, A. C., Pinson, B., Praefcke, G. J. K., Langer, T., & Escobar‐Henriques, M. (2011) · Journal of Cell Science · doi:10.1242/jcs.073080 · Cited by 98
Discovering cellular protein‐protein interactions: Technological strategies and opportunities
Titeca, K., Lemmens, I. H., Tavernier, J. H., & Eyckerman, S. (2018) · Mass Spectrometry Reviews · doi:10.1002/mas.21574 · Cited by 95
Self-citationProtein–protein interaction predictions using text mining methods
Papanikolaou, N., Pavlopoulos, G. A., Θεοδοσίου, Θ., & Iliopoulos, I. (2014) · Methods · doi:10.1016/j.ymeth.2014.10.026 · Cited by 91
Predicting tissue-specific gene expression from whole blood transcriptome
Basu, M., Wang, K., Ruppin, E., & Hannenhalli, S. S. (2021) · Science Advances · doi:10.1126/sciadv.abd6991 · Cited by 93
Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions
Betts, M. J., Lu, Q., Jiang, Y., Drusko, A., Wichmann, O., Utz, M., Valtierra-Gutiérrez, I. A., Schlesner, M., Jäger, N., Jones, D., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1094 · Cited by 90
Friedman, A. A., Tucker, G., Singh, R., Yan, D., Vinayagam, A., Hu, Y., Binari, R. C., Hong, P., Sun, X., Porto, M., et al. (2011) · Science Signaling · doi:10.1126/scisignal.2002029 · Cited by 90
A New Method for the Discovery of Essential Proteins
Zhang, X., Xu, J., & Xiao, W. (2013) · PLoS ONE · doi:10.1371/journal.pone.0058763 · Cited by 89
Promoter-Based Integration in Plant Defense Regulation
Li, B., Gaudinier, A., Tang, M., Taylor‐Teeples, M., Nham, N. T., Ghaffari, C., Benson, D. S., Steinmann, M., Gray, J. A., Brady, S. M., et al. (2014) · PLANT PHYSIOLOGY · doi:10.1104/pp.114.248716 · Cited by 87
Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development
Kazemian, M., Pham, H., Wolfe, S. A., Brodsky, M. H., & Sinha, S. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt598 · Cited by 87
Rao, B. S., & Parker, R. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1712396114 · Cited by 87
The post-genomic era of biological network alignment
Faisal, F. E., Meng, L., Crawford, J., & Milenković, T. (2015) · EURASIP Journal on Bioinformatics and Systems Biology · doi:10.1186/s13637-015-0022-9 · Cited by 85
Detecting temporal protein complexes from dynamic protein-protein interaction networks
Ou-Yang, L., Dai, D., Li, X., Wu, M., Zhang, X.-F., & Yang, P. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-335 · Cited by 86
Machine-learning techniques for the prediction of protein–protein interactions
Sarkar, D., & Saha, S. (2019) · Journal of Biosciences · doi:10.1007/s12038-019-9909-z · Cited by 89
Precision and recall estimates for two-hybrid screens
Huang, H., & Bader, J. S. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn640 · Cited by 86
A Comprehensive Drosophila melanogaster Transcription Factor Interactome
Shokri, L., Inukai, S., Hafner, A., Weinand, K., Hens, K., Vedenko, A., Gisselbrecht, S. S., Dainese, R., Bischof, J., Furger, E., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.03.071 · Cited by 86
The emergence of protein complexes: quaternary structure, dynamics and allostery
Perica, T., Marsh, J. A., Sousa, F. L., Natan, E., Colwell, L. J., Ahnert, S. E., & Teichmann, S. A. (2012) · Biochemical Society Transactions · doi:10.1042/bst20120056 · Cited by 87
Inferring Orthologs: Open Questions and Perspectives
Tekaia, F. (2016) · Genomics Insights · doi:10.4137/gei.s37925 · Cited by 84
Mapping technology space by normalizing patent networks
Alstott, J., Triulzi, G., Yan, B., & Luo, J. (2016) · Scientometrics · doi:10.1007/s11192-016-2107-y · Cited by 84
Hu, L., Yang, S., Luo, X., Yuan, H., Sedraoui, K., & Zhou, M. (2021) · IEEE/CAA Journal of Automatica Sinica · doi:10.1109/jas.2021.1004198 · Cited by 84
Protein‐protein interaction networks as miners of biological discovery
Wang, S., Wu, R., Lü, J., Jiang, Y., Huang, T., & Cai, Y. (2022) · PROTEOMICS · doi:10.1002/pmic.202100190 · Cited by 92
Singh, R. P., & Jwa, N. (2013) · Plant Cell Reports · doi:10.1007/s00299-013-1437-y · Cited by 84
Lewis, J. D., Wan, J. W., Ford, R., Gong, Y., Fung, P., Nahal-Bose, H. K., Wang, P. W., Desveaux, D., & Guttman, D. S. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-8 · Cited by 84
Gene Coexpression Networks for the Analysis of DNA Microarray Data
Weirauch, M. T. (2011) · Wiley eBooks · doi:10.1002/9783527638079.ch11 · Cited by 87
Duan, X., Yang, Y., Chen, Y.-H., Arenz, J., Rangi, G. K., Zhao, X., & Ye, H. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m809139200 · Cited by 83
Coiled-coil networking shapes cell molecular machinery
Wang, Y., Zhang, X., Zhang, H., Lu, Y., Huang, H., Dong, X., Chen, J., Dong, J., Yang, X., Hang, H., et al. (2012) · Molecular Biology of the Cell · doi:10.1091/mbc.e12-05-0396 · Cited by 85
Network Structure, Metadata, and the Prediction of Missing Nodes and Annotations
Hric, D., Peixoto, T. P., & Fortunato, S. (2016) · Physical Review X · doi:10.1103/physrevx.6.031038 · Cited by 90
Intelligence, Cognition, and Language of Green Plants
TREWAVAS, A. J. (2016) · Frontiers in Psychology · doi:10.3389/fpsyg.2016.00588 · Cited by 85
Modulating transcription factor activity: Interfering with protein-protein interaction networks
François, M., Donovan, P., & Fontaine, F. R. (2018) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2018.07.019 · Cited by 83
Luo, X., You, Z., Zhou, M., Li, S., LEUNG, H. K. N., Xia, Y., & Zhu, Q. (2015) · Scientific Reports · doi:10.1038/srep07702 · Cited by 82
The methylproteome and the intracellular methylation network
Erce, M. A., Pang, C. N. I., Hart‐Smith, G., & Wilkins, M. R. (2012) · PROTEOMICS · doi:10.1002/pmic.201100397 · Cited by 83
Kim, W., & Marcotte, E. M. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000232 · Cited by 82
Gachomo, E. W., Jiménez-López, J. C., Baptiste, L. J., & Kotchoni, S. O. (2014) · BMC Plant Biology · doi:10.1186/1471-2229-14-37 · Cited by 82
Emergent stability in complex network dynamics
Meena, C., Hens, C., Acharyya, S., Haber, S., Boccaletti, S., & Barzel, B. (2023) · Nature Physics · doi:10.1038/s41567-023-02020-8 · Cited by 88
Graphlet-based edge clustering reveals pathogen-interacting proteins
Solava, R. W., Michaels, R. P., & Milenković, T. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts376 · Cited by 80
Signaling and Communication in Plants
Mugnai, S. (2011) · Frontiers in artificial intelligence and applications · doi:10.3233/978-1-60750-972-1-205 · Cited by 81
Rees, J. S., Lowe, N., Armean, I. M., Roote, J., Johnson, G., Drummond, E., Spriggs, H. F., Ryder, E. J., Russell, S. R. H., Johnston, D. S., et al. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.002386 · Cited by 79
An Evolutionary Multiobjective Optimization Based Fuzzy Method for Overlapping Community Detection
Tian, Y., Yang, S., & Zhang, X. (2019) · IEEE Transactions on Fuzzy Systems · doi:10.1109/tfuzz.2019.2945241 · Cited by 79
Mapping transcription factor interactome networks using HaloTag protein arrays
Yazaki, J., Galli, M., Kim, A. Y., Nito, K., Alemán, F., Chang, K. N., Carvunis, A., Quan, R., Nguyen, H. P., Song, L., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1603229113 · Cited by 77
Self-citationMaximizing binary interactome mapping with a minimal number of assays
Choi, S. G., Olivet, J., Cassonnet, P., Vidalain, P., Luck, K., Lambourne, L., Spirohn, K., Lemmens, I. H., Santos, M. D., Demeret, C., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-11809-2 · Cited by 76
Self-citationProtein complementation assays: Approaches for the in vivo analysis of protein interactions
Morell, M., Ventura, S., & Avilés, F. X. (2009) · FEBS Letters · doi:10.1016/j.febslet.2009.03.002 · Cited by 78
Luo, J., & Qi, Y. (2015) · PLoS ONE · doi:10.1371/journal.pone.0131418 · Cited by 77
Local versus global biological network alignment
Meng, L., Striegel, A., & Milenković, T. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw348 · Cited by 75
A Novel Algorithm for the Precise Calculation of the Maximal Information Coefficient
Zhang, Y., Jia, S., Huang, H., Qiu, J., & Zhou, C.-J. (2014) · Scientific Reports · doi:10.1038/srep06662 · Cited by 77
Chen, C., Huang, B., Anderson, J. T., & Byström, A. S. (2011) · PLoS ONE · doi:10.1371/journal.pone.0020783 · Cited by 77
Enhanced Protein-Protein Interaction Discovery via AlphaFold-MultimerPreprint
Kim, A., Hu, Y., Comjean, A., Rodiger, J., Mohr, S. E., & Perrimon, N. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.19.580970 · Cited by 79
Shchepachev, V., Wischnewski, H., Missiaglia, E., Soneson, C., & Azzalin, C. M. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.08.031 · Cited by 76
Rodrigo, G., Carrera, J., Ruíz‐Ferrer, V., del Toro, F. J., Llave, C., Voinnet, O., & Elena, S. F. (2012) · PLoS ONE · doi:10.1371/journal.pone.0040526 · Cited by 74
Identification of FAM111A as an SV40 Host Range Restriction and Adenovirus Helper Factor
Fine, D. A., Rozenblatt–Rosen, O., Padi, M., Korkhin, A., James, R. L., Adelmant, G., Yoon, R., Guo, L., Berrios, C. J., Zhang, Y., et al. (2012) · PLoS Pathogens · doi:10.1371/journal.ppat.1002949 · Cited by 76
Self-citationNonspecific binding limits the number of proteins in a cell and shapes their interaction networks
Johnson, M. E., & Hummer, G. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1010954108 · Cited by 74
Protein‐protein interactions: Making sense of networks via graph‐theoretic modeling
Pržulj, N. (2010) · BioEssays · doi:10.1002/bies.201000044 · Cited by 78
Hubs and bottlenecks in plant molecular signalling networks
Dietz, K., Jacquot, J., & Harris, G. C. (2010) · New Phytologist · doi:10.1111/j.1469-8137.2010.03502.x · Cited by 78
Structural characterization of the Get4/Get5 complex and its interaction with Get3
Chartron, J. W., Suloway, C. J. M., Zaslaver, M., & Clemons, W. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1006036107 · Cited by 76
Curating the innate immunity interactome
Lynn, D. J., Chan, C. C., Naseer, M., Yau, M., Lo, R., Sribnaia, A., Ring, G., Que, J., Wee, K., Winsor, G. L., et al. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-117 · Cited by 75
How Perfect Can Protein Interactomes Be?
Levy, E. D., Landry, C. R., & Michnick, S. W. (2009) · Science Signaling · doi:10.1126/scisignal.260pe11 · Cited by 74
Chen, Y., Stabryla, L. M., & Wei, N. (2016) · Applied and Environmental Microbiology · doi:10.1128/aem.03718-15 · Cited by 77
Chen, S., Fragoza, R., Klei, L., Liu, Y., Wang, J., Roeder, K., Devlin, B., & Yu, H. (2018) · Nature Genetics · doi:10.1038/s41588-018-0130-z · Cited by 75
Self-citationA kaleidoscopic view of the Arabidopsis core cell cycle interactome
Leene, J. V., Boruc, J., Jaeger, G. D., Russinova, E., & Veylder, L. D. (2011) · Trends in Plant Science · doi:10.1016/j.tplants.2010.12.004 · Cited by 73
Environmental robustness of the global yeast genetic interaction network
Costanzo, M., Hou, J., Messier, V., Nelson, J., Rahman, M., VanderSluis, B., Wang, W., Pons, C., Ross, C., Ušaj, M., et al. (2021) · Science · doi:10.1126/science.abf8424 · Cited by 75
Self-citationControlling Directed Protein Interaction Networks in Cancer
Kanhaiya, K., Czeizler, E., Gratie, C., & Petre, I. (2017) · Scientific Reports · doi:10.1038/s41598-017-10491-y · Cited by 73
PAIR: the predicted Arabidopsis interactome resource
Lin, M., Shen, X., & Chen, X. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq938 · Cited by 72
Reviving a failed network through microscopic interventions
Sanhedrai, H., Gao, J., Bashan, A., Schwartz, M., Havlin, S., & Barzel, B. (2022) · Nature Physics · doi:10.1038/s41567-021-01474-y · Cited by 71
Goel, R., Muthusamy, B., Pandey, A., & Prasad, T. S. K. (2010) · Molecular Biotechnology · doi:10.1007/s12033-010-9336-8 · Cited by 73
Detecting cohesive and 2-mode communities indirected and undirected networks
Yang, J., McAuley, J., & Leskovec, J. (2014) · ACM International Conference on Web Search and Data Mining (WSDM) · doi:10.1145/2556195.2556243 · Cited by 72
Pascual, F. L., Soto-Cardalda, A., & Carman, G. M. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m113.525766 · Cited by 72
Revisiting the negative example sampling problem for predicting protein–protein interactions
Park, Y., & Marcotte, E. M. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr514 · Cited by 72
A general Evolutionary Framework for different classes of Critical Node Problems
Aringhieri, R., Grosso, A., Hosteins, P., & Scatamacchia, R. (2016) · Engineering Applications of Artificial Intelligence · doi:10.1016/j.engappai.2016.06.010 · Cited by 72
Mapping, modeling, and characterization of protein–protein interactions on a proteomic scale
Cafarelli, T. M., Desbuleux, A., Wang, Y., Choi, S. G., Ridder, D. D., & Vidal, M. (2017) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2017.05.003 · Cited by 75
Self-citationFunctional wiring of the yeast kinome revealed by global analysis of genetic network motifsPreprint
Sharifpoor, S., van Dyk, D., Costanzo, M., Baryshnikova, A., Friesen, H., Douglas, A. C., Youn, J.-Y., VanderSluis, B., Myers, C. L., Papp, B., et al. (2012) · Genome Research · doi:10.1101/gr.129213.111 · Cited by 71
Self-citationThe C-terminus of Utp4, mutated in childhood cirrhosis, is essential for ribosome biogenesis
Freed, E. F., & Baserga, S. J. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq185 · Cited by 75
Chang, X., Xu, T., Li, Y., & Wang, K. (2013) · Scientific Reports · doi:10.1038/srep01691 · Cited by 72
Host-pathogen interactome mapping for HTLV-1 and -2 retroviruses
Simonis, N., Rual, J.-F. M., Lemmens, I. H., Boxus, M., Hirozane-Kishikawa, T., Gatot, J., Dricot, A., Hao, T., Vertommen, D., Legros, S., et al. (2012) · Retrovirology · doi:10.1186/1742-4690-9-26 · Cited by 76
Self-citationXu, Z., Li, T., Li, E., Chen, K., Ding, Z., Qin, J. G., Chen, L., & Ye, J. (2015) · Fish & Shellfish Immunology · doi:10.1016/j.fsi.2015.12.005 · Cited by 71
Putting genetic interactions in context through a global modular decompositionPreprint
Bellay, J., Atluri, G., Sing, T. L., Toufighi, K., Costanzo, M., Ribeiro, P. S. M., Pandey, G. S., Baller, J. A., VanderSluis, B., Michaut, M., et al. (2011) · Genome Research · doi:10.1101/gr.117176.110 · Cited by 72
Self-citationFinding local communities in protein networks
Voevodski, K., Teng, S., & Xia, Y. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-297 · Cited by 70
Proteomic approaches to the study of papillomavirus–host interactions
White, E. A., & Howley, P. M. (2012) · Virology · doi:10.1016/j.virol.2012.09.046 · Cited by 71
Mosca, R., Pons, C., Fernández‐Recio, J., & Aloy, P. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000490 · Cited by 70
SH3 interactome conserves general function over specific form
Xin, X., Gfeller, D., Cheng, J. C., Tonikian, R., Sun, L., Guo, A., Lopez, L., Pavlenco, A., Akintobi, A., Zhang, Y., et al. (2013) · Molecular Systems Biology · doi:10.1038/msb.2013.9 · Cited by 64
Self-citationAn ORFeome of rice E3 ubiquitin ligases for global analysis of the ubiquitination interactome
Wang, R., You, X., Zhang, C., Fang, H., Wang, M., Zhang, F., Kang, H., Xu, X. J., Liu, Z., Wang, J., et al. (2022) · Genome biology · doi:10.1186/s13059-022-02717-8 · Cited by 72
Structure and regulatory networks of WD40 protein in plants
Mishra, A. K., Puranik, S., & Prasad, M. (2012) · Journal of Plant Biochemistry and Biotechnology · doi:10.1007/s13562-012-0134-1 · Cited by 71
Communities and bottlenecks: Trees and treelike networks have high modularity
Bagrow, J. P. (2012) · Physical Review E · doi:10.1103/physreve.85.066118 · Cited by 71
Metadata
- Authors
- Yu, H., Braun, P., Yıldırım, M. A., Lemmens, I., Venkatesan, K., Sahalie, J., Hirozane-Kishikawa, T., Gebreab, F., Li, N., Simonis, N., Hao, T., Rual, J.-F., Dricot, A., Vazquez, A., Murray, R. R., Simon, C., Tardivo, L., Tam, S., Svrzikapa, N., Fan, C., de Smet, A.-S., Motyl, A., Hudson, M. E., Park, J., Xin, X., Cusick, M. E., Moore, T., Boone, C., Snyder, M., Roth, F. P., Barabási, A.-L., Tavernier, J., Hill, D. E., & Vidal, M.
- Affiliations
- Harvard University (US)
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02115, USA.
- Northeastern University (US)
- Corresponding author
- Yu, Haiyuan
- Yıldırım, Muhammed A.
- Vidal, Marc
- ORCID
- Venue
- Science
- Published
- 2008-10-03
- Volume
- 322
- Issue
- 5898
- Pages
- 104-110
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC2746753
- OpenAlex
- W2109248504
- Cited by
- 1,392
- References
- 45
- Citations by year
- 2026: 18 · 2025: 26 · 2024: 29 · 2023: 34 · 2022: 63 · 2021: 55 · 2020: 66 · 2019: 65 · 2018: 67 · 2017: 72 · 2016: 68 · 2015: 78 · 2014: 79 · 2013: 122 · 2012: 172
- FWCI
- 51.78
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Ghent University Academic Bibliography (Ghent University) (submittedVersion)
- Dépôt institutionnel de l'Université libre de Bruxelles (Université Libre de Bruxelles) (submittedVersion, other-oa)
- Funders
- U.S. Public Health Service (U01A1070499-01)
- National Human Genome Research Institute (R01HG001715, R01HG003224, HG003224)
- National Cancer Institute (U56CA113004)
- National Institute of Allergy and Infectious Diseases (U01AI070499)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Keywords
- yeast interactome, protein-protein interaction network, yeast two-hybrid screening, affinity purification mass spectrometry, protein complexes, essential proteins, protein connectivity, pleiotropy, network topology
- MeSH terms
- Protein Binding, Saccharomyces cerevisiae, Mass Spectrometry, Transcription Factors, Signal Transduction, Computational Biology, Proteome, Two-Hybrid System Techniques, Protein Interaction Mapping, Saccharomyces cerevisiae Proteins, Protein Array Analysis, Proteomics, Gene Regulatory Networks, Metabolic Networks and Pathways
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
