Predicting protein–protein interactions from the molecular to the proteome level

O Keskin, N Tuncbag, A Gursoy - Chemical reviews, 2016 - ACS Publications
Identification of protein–protein interactions (PPIs) is at the center of molecular biology
considering the unquestionable role of proteins in cells. Combinatorial interactions result in …

A review of bioinformatics tools and web servers in different microarray platforms used in cancer research

RH Cathryn, SU Kumar, S Younes, H Zayed… - Advances in protein …, 2022 - Elsevier
Over the past decade, conventional lab work strategies have gradually shifted from being
limited to a laboratory setting towards a bioinformatics era to help manage and process the …

Integration of biological networks and gene expression data using Cytoscape

MS Cline, M Smoot, E Cerami, A Kuchinsky… - Nature protocols, 2007 - nature.com
Cytoscape is a free software package for visualizing, modeling and analyzing molecular and
genetic interaction networks. This protocol explains how to use Cytoscape to analyze the …

Relaxation response induces temporal transcriptome changes in energy metabolism, insulin secretion and inflammatory pathways

MK Bhasin, JA Dusek, BH Chang, MG Joseph… - PloS one, 2013 - journals.plos.org
The relaxation response (RR) is the counterpart of the stress response. Millennia-old
practices evoking the RR include meditation, yoga and repetitive prayer. Although RR …

ConsensusPathDB—a database for integrating human functional interaction networks

A Kamburov, C Wierling, H Lehrach… - Nucleic acids …, 2009 - academic.oup.com
ConsensusPathDB is a database system for the integration of human functional interactions.
Current knowledge of these interactions is dispersed in more than 200 databases, each …

iRefIndex: a consolidated protein interaction database with provenance

S Razick, G Magklaras, IM Donaldson - BMC bioinformatics, 2008 - Springer
Background Interaction data for a given protein may be spread across multiple databases.
We set out to create a unifying index that would facilitate searching for these data and that …

MINT, the molecular interaction database: 2009 update

A Ceol, A Chatr Aryamontri, L Licata… - Nucleic acids …, 2010 - academic.oup.com
ABSTRACT MINT (http://mint. bio. uniroma2. it/mint) is a public repository for molecular
interactions reported in peer-reviewed journals. Since its last report, MINT has grown …

Integrated network analysis platform for protein-protein interactions

J Wu, T Vallenius, K Ovaska, J Westermarck… - Nature …, 2009 - nature.com
There is an increasing demand for network analysis of protein-protein interactions (PPIs).
We introduce a web-based protein interaction network analysis platform (PINA), which …

Why not?

A Chapman, HV Jagadish - Proceedings of the 2009 ACM SIGMOD …, 2009 - dl.acm.org
As humans, we have expectations for the results of any action, eg we expect at least one
student to be returned when we query a university database for student records. When these …

Making database systems usable

HV Jagadish, A Chapman, A Elkiss… - Proceedings of the …, 2007 - dl.acm.org
Database researchers have striven to improve the capability of a database in terms of both
performance and functionality. We assert that the usability of a database is as important as …