Fundamentals of protein interaction network map**

J Snider, M Kotlyar, P Saraon, Z Yao… - Molecular systems …, 2015 - embopress.org
Studying protein interaction networks of all proteins in an organism (“interactomes”) remains
one of the major challenges in modern biomedicine. Such information is crucial to …

Characterizing endogenous protein complexes with biological mass spectrometry

R Rogawski, M Sharon - Chemical reviews, 2021 - ACS Publications
Biological mass spectrometry (MS) encompasses a range of methods for characterizing
proteins and other biomolecules. MS is uniquely powerful for the structural analysis of …

Spectral clustering on protein-protein interaction networks via constructing affinity matrix using attributed graph embedding

K Berahmand, E Nasiri, Y Li - Computers in Biology and Medicine, 2021 - Elsevier
The identification of protein complexes in protein-protein interaction networks is the most
fundamental and essential problem for revealing the underlying mechanism of biological …

Thermal proximity coaggregation for system-wide profiling of protein complex dynamics in cells

CSH Tan, KD Go, X Bisteau, L Dai, CH Yong, N Prabhu… - Science, 2018 - science.org
Proteins differentially interact with each other across cellular states and conditions, but an
efficient proteome-wide strategy to monitor them is lacking. We report the application of …

An effective link-based clustering algorithm for detecting overlap** protein complexes in protein-protein interaction networks

L Hu, J Zhang, X Pan, X Luo… - IEEE Transactions on …, 2021 - ieeexplore.ieee.org
Protein complexes are one most important kind of functional modules for biological
processes in cells. In this regard, their detection is vital for understanding the principle of cell …

Computational approaches for detecting protein complexes from protein interaction networks: a survey

X Li, M Wu, CK Kwoh, SK Ng - BMC genomics, 2010 - Springer
Background Most proteins form macromolecular complexes to perform their biological
functions. However, experimentally determined protein complex data, especially of those …

Temporal dynamics of protein complex formation and dissociation during human cytomegalovirus infection

Y Hashimoto, X Sheng, LA Murray-Nerger… - Nature …, 2020 - nature.com
The co-evolution and co-existence of viral pathogens with their hosts for millions of years is
reflected in dynamic virus-host protein-protein interactions (PPIs) that are intrinsic to the …

Identifying protein complexes and functional modules—from static PPI networks to dynamic PPI networks

B Chen, W Fan, J Liu, FX Wu - Briefings in bioinformatics, 2014 - academic.oup.com
Cellular processes are typically carried out by protein complexes and functional modules.
Identifying them plays an important role for our attempt to reveal principles of cellular …

Efficiently detecting protein complexes from protein interaction networks via alternating direction method of multipliers

L Hu, X Yuan, X Liu, S **ong… - IEEE/ACM transactions on …, 2018 - ieeexplore.ieee.org
Protein complexes are crucial in improving our understanding of the mechanisms employed
by proteins. Various computational algorithms have thus been proposed to detect protein …

From protein-protein interactions to protein co-expression networks: a new perspective to evaluate large-scale proteomic data

D Vella, I Zoppis, G Mauri, P Mauri… - EURASIP Journal on …, 2017 - Springer
The reductionist approach of dissecting biological systems into their constituents has been
successful in the first stage of the molecular biology to elucidate the chemical basis of …