Diversity in Genetic In Vivo Methods for Protein-Protein Interaction Studies: from the Yeast Two-Hybrid System to the Mammalian Split-Luciferase System

B Stynen, H Tournu, J Tavernier… - … and molecular biology …, 2012 - Am Soc Microbiol
The yeast two-hybrid system pioneered the field of in vivo protein-protein interaction
methods and undisputedly gave rise to a palette of ingenious techniques that are constantly …

Network analysis and in silico prediction of protein–protein interactions with applications in drug discovery

Y Murakami, LP Tripathi, P Prathipati… - Current opinion in …, 2017 - Elsevier
Highlights•Protein–protein interactions (PPIs) have emerged as promising targets for drug
discovery.•PPI network (PPIN)-based analyses can reveal genotype–phenotype …

Correlation AnalyzeR: functional predictions from gene co-expression correlations

HE Miller, AJR Bishop - BMC bioinformatics, 2021 - Springer
Background Co-expression correlations provide the ability to predict gene functionality
within specific biological contexts, such as different tissue and disease conditions. However …

A novel link prediction algorithm for reconstructing protein–protein interaction networks by topological similarity

C Lei, J Ruan - Bioinformatics, 2013 - academic.oup.com
Motivation: Recent advances in technology have dramatically increased the availability of
protein–protein interaction (PPI) data and stimulated the development of many methods for …

Homology-based prediction of interactions between proteins using averaged one-dependence estimators

Y Murakami, K Mizuguchi - BMC bioinformatics, 2014 - Springer
Background Identification of protein-protein interactions (PPIs) is essential for a better
understanding of biological processes, pathways and functions. However, experimental …

Neuroblastoma tyrosine kinase signaling networks involve FYN and LYN in endosomes and lipid rafts

J Palacios-Moreno, L Foltz, A Guo… - PLoS computational …, 2015 - journals.plos.org
Protein phosphorylation plays a central role in creating a highly dynamic network of
interacting proteins that reads and responds to signals from growth factors in the cellular …

BIPS: BIANA Interolog Prediction Server. A tool for protein–protein interaction inference

J Garcia-Garcia, S Schleker… - Nucleic acids …, 2012 - academic.oup.com
Protein–protein interactions (PPIs) play a crucial role in biology, and high-throughput
experiments have greatly increased the coverage of known interactions. Still, identification of …

Using FlyBase, a Database of Drosophila Genes and Genomes

SJ Marygold, MA Crosby, JL Goodman… - … : Methods and Protocols, 2016 - Springer
For nearly 25 years, FlyBase (flybase. org) has provided a freely available online database
of biological information about Drosophila species, focusing on the model organism D …

Dissecting the gene network of dietary restriction to identify evolutionarily conserved pathways and new functional genes

D Wuttke, R Connor, C Vora, T Craig, Y Li, S Wood… - 2012 - journals.plos.org
Dietary restriction (DR), limiting nutrient intake from diet without causing malnutrition, delays
the aging process and extends lifespan in multiple organisms. The conserved life-extending …

Pogo-like Transposases Have Been Repeatedly Domesticated into CENP-B-Related Proteins

L Mateo, J Gonzalez - Genome biology and evolution, 2014 - academic.oup.com
The centromere is a chromatin region that is required for accurate inheritance of eukaryotic
chromosomes during cell divisions. Among the different centromere-associated proteins …