Protein function in the post-genomic era

By David S. Eisenberg, Edward M. Marcotte, Ioannis Xenarios, Todd O. Yeates. Nature, 2000

790 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/8de3191a56a122ca746183a7120d90ed2a1cfcff

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Citations in the corpus

News from the protein mutability landscape. (2013, background): “The most important function of a protein can therefore be defined as its role within an interaction pathway [49].”
Protein–protein interaction and quaternary structure (2008, background): “Indeed, the biological function of a protein can be seen as defined by the context of its interactions in the cell, and inappropriate interactions can lead to diseases (Alberts, 1998 ; Eisenberg et al. 2000).”
Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. (2003, neutral): “2,3 Coupled with computational approaches, significant efforts are undertaken for developing high-throughput experimental technologies and producing large-scale data in transcriptome, 4 proteome, 5 and metabolome analyses.”
What is Bioinformatics? A Proposed Definition and Overview of the Field (2001, background): “Conventional wisdom is that gene products that interact with each other are more likely to have similar expression profiles than if they do not [101, 102].”
Analyzing and modeling real-world phenomena with complex networks: a survey of applications (2007, methodology): “This limitation has motivated the development of many other methods, including bioc hemical techniques such as affinity [295] and molecular size-based chromatography, affinit y blotting, immuno-precipitation and cross-linking [317, 321, 322, 323].”
Human knockouts and phenotypic analysis in a cohort with a high rate of consanguinity (2017, positive): “…proteins involved in parathyroid hormone or osteoclast signalling including calcium/calmodulin-dependent protein kinase II (CAMK2) alpha, beta, and delta subunits, cAMP-regulated phosphoprotein 19, and signal transducer and activator of transcription (STAT) 1, 3, and 6 (Supplementary Table 5).”
Prolinks: a database of protein functional linkages derived from coevolution (2004, background): “A more complete understanding of protein function requires the identification of interacting partners: interacting subunits if the protein is a component of a molecular complex, and pathway members if the protein participates in a metabolic or signal transduction pathway [1].”
Correlated sequence-signatures as markers of protein-protein interaction. (2001, background): “These approaches do not rely directly on sequence similarity between genes (or their products), but rather use different types of information to reveal the functional relationships between molecules.(15,16) For example, a systematic comparison of the gene order among different genomes has revealed t”
From Instance-level Constraints to Space-Level Constraints: Making the Most of Prior Knowledge in Data Clustering (2002, background): “For instance, for the task of protein function prediction, genome sequence data can be augmented by knowledge about functional links between proteins (Eisenberg et al., 2000).”
Recent progress and future directions in protein-protein docking. (2008, neutral): “1389-2037/08 $55.00+.00 © 2008 Bentham Science Publishers Ltd. Keywords: Protein-protein docking, protein-protein interactions, docking algorithms, data-driven docking, molecular dynamics, protein structure databases, protein interface prediction, CAPRI.”
The challenges of in silico biology (2000, background): “Extrapolation between genomes will then most likely accelerate the definition of what amounts to a “parts catalog” of cellular components in a large number of organism”
Relating whole-genome expression data with protein-protein interactions. (2002, background): “Christendat et al. 2000a; Christendat et al. 2000b; Eisenberg et al. 2000; Emili and”
Computational prediction of proteotypic peptides for quantitative proteomics (2007, background): “, description of functional aspects of proteins by sequence domains and motif”