Expanding interactome analyses beyond model eukaryotes

K James, A Wipat, SJ Cockell - Briefings in Functional Genomics, 2022 - academic.oup.com
Interactome analyses have traditionally been applied to yeast, human and other model
organisms due to the availability of protein–protein interaction data for these species …

Building and analyzing protein interactome networks by cross-species comparisons

AM Wiles, M Doderer, J Ruan, TT Gu, D Ravi… - BMC systems …, 2010 - Springer
Background A genomic catalogue of protein-protein interactions is a rich source of
information, particularly for exploring the relationships between proteins. Numerous systems …

New insights into protein-protein interaction data lead to increased estimates of the S. cerevisiae interactome size

L Sambourg, N Thierry-Mieg - BMC bioinformatics, 2010 - Springer
Background As protein interactions mediate most cellular mechanisms, protein-protein
interaction networks are essential in the study of cellular processes. Consequently, several …

Assessing reliability of protein-protein interactions by integrative analysis of data in model organisms

X Lin, M Liu, X Chen - BMC bioinformatics, 2009 - Springer
Background Protein-protein interactions play vital roles in nearly all cellular processes and
are involved in the construction of biological pathways such as metabolic and signal …

Inferring interaction networks from multi-omics data

JS Hawe, FJ Theis, M Heinig - Frontiers in genetics, 2019 - frontiersin.org
A major goal in systems biology is a comprehensive description of the entirety of all complex
interactions between different types of biomolecules—also referred to as the interactome …

Protein–protein interactions more conserved within species than across species

S Mika, B Rost - PLoS computational biology, 2006 - journals.plos.org
Experimental high-throughput studies of protein–protein interactions are beginning to
provide enough data for comprehensive computational studies. Today, about ten large data …

Predicting whole genome protein interaction networks from primary sequence data in model and non-model organisms using ENTS

E Rodgers-Melnick, M Culp, SP DiFazio - BMC genomics, 2013 - Springer
Background The large-scale identification of physical protein-protein interactions (PPIs) is
an important step toward understanding how biological networks evolve and generate …

Complementing the eukaryotic protein interactome

R Pesch, R Zimmer - PloS One, 2013 - journals.plos.org
Protein interaction networks are important for the understanding of regulatory mechanisms,
for the explanation of experimental data and for the prediction of protein functions …

Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions

V van Noort, B Snel, MA Huynen - Genome Biology, 2007 - Springer
Background In the post-genomic era various functional genomics, proteomics and
computational techniques have been developed to elucidate the protein interaction network …

Open source tool for prediction of genome wide protein-protein interaction network based on ortholog information

CS Pedamallu, J Posfai - Source code for biology and medicine, 2010 - Springer
Background Protein-protein interactions are crucially important for cellular processes.
Knowledge of these interactions improves the understanding of cell cycle, metabolism …