Evidence for dynamically organized modularity in the yeast protein–protein interaction network

By Jing-Dong J. Han, Nicolas Bertin, Tong Hao, Debra S. Goldberg, G. Berriz, Lan V. Zhang, D. Dupuy, A. Walhout, Michael E. Cusick, Frederick P. Roth and 1 more. 2004

1,807 citations recorded by the source corpus.

Subfields: Molecular Biology

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Citations in the corpus

Network Motif Discovery Using Subgraph Enumeration and Symmetry-Breaking (2007, methodology): “cerevisiae[4], and does not appear at all in random ensembles which preserve the degree distribution and the distribution of 3node subgraphs.”
Molecular networks as sensors and drivers of common human diseases (2009, background): “Interaction, or association, networks, which have recently become widely used in the biological community, are formed by considering only pairwise relationships between genes, including protein interaction”
A human protein-protein interaction network: a resource for annotating the proteome. (2005, positive): “This also suggests that the interaction network has two levels of organization, local clustering, potentially representing protein complexes or functional modules, and more global connectivity mediated via hubs, conceivable as higher-order communication points between protein complexes ( Han et al.,”
Toward a Comprehensive Atlas of the Physical Interactome of Saccharomyces cerevisiae*S (2007, result): “Using the true positive and true negative sets of protein pairs described above not only allowed us to compare the processed results of this consolidated dataset to previous high-throughput datasets, but it also provided an opportunity to compare our new results to those obtained in small-scale expe”
The model organism as a system: integrating 'omics' data sets (2006, background): “, are also extending these analyses to reflect the dynamic properties of the network by assessing topological features under various environmental condition”
Structural systems biology: modelling protein interactions (2006, background): “By combining interaction maps and expression data, it has recently been argued that some of these highly connected molecules are 'party hubs', which tend to interact with other proteins continuously throughout the cell cycle, whereas others are 'date hubs', which make specific connections at particu”
Reverse engineering of regulatory networks in human B cells (2005, background): “numbers in the interval [0,1], preserving their original order.”
Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality (2008, methodology): “Furthermore, it has been proposed that ‘‘party hubs represent integral elements within distinct modules’’ and ‘‘tend to function at a lower level of the organization of the proteome’’ [35].”
Integrative approaches for finding modular structure in biological networks (2013, background): “Molecular interactions can change dramatically in response to cellular cues, developmental stages, environmental stresses, pharmacological treatments and disease states 32,100,129,132,133 .”
Network modeling links breast cancer susceptibility and centrosome dysfunction. (2007, methodology): “For the BCN modeling, we integrated, first, gene expression profiling similarity above a given threshold, as determined by the PCC, from a compendium of Saccharomyces cerevisiae”