Toward the dynamic interactome: it's about time

TM Przytycka, M Singh, DK Slonim - Briefings in bioinformatics, 2010 - academic.oup.com
Dynamic molecular interactions play a central role in regulating the functioning of cells and
organisms. The availability of experimentally determined large-scale cellular networks …

Recent advances in clustering methods for protein interaction networks

J Wang, M Li, Y Deng, Y Pan - BMC genomics, 2010 - Springer
The increasing availability of large-scale protein-protein interaction data has made it
possible to understand the basic components and organization of cell machinery from the …

[图书][B] Protein interaction networks: computational analysis

A Zhang - 2009 - books.google.com
The analysis of protein-protein interactions is fundamental to the understanding of cellular
organization, processes, and functions. Recent large-scale investigations of protein-protein …

Semantic integration to identify overlapping functional modules in protein interaction networks

YR Cho, W Hwang, M Ramanathan, A Zhang - BMC bioinformatics, 2007 - Springer
Background The systematic analysis of protein-protein interactions can enable a better
understanding of cellular organization, processes and functions. Functional modules can be …

Protein complex identification by supervised graph local clustering

Y Qi, F Balem, C Faloutsos, J Klein-Seetharaman… - …, 2008 - academic.oup.com
Motivation: Protein complexes integrate multiple gene products to coordinate many
biological functions. Given a graph representing pairwise protein interaction data one can …

Current and future directions in network biology

M Zitnik, MM Li, A Wells, K Glass, DM Gysi… - arXiv preprint arXiv …, 2023 - arxiv.org
Network biology, an interdisciplinary field at the intersection of computational and biological
sciences, is critical for deepening understanding of cellular functioning and disease. While …

Protein-to-protein interactions: Technologies, databases, and algorithms

M Cannataro, PH Guzzi, P Veltri - ACM Computing Surveys (CSUR), 2010 - dl.acm.org
Studying proteins and their structures has an important role for understanding protein
functionalities. Recently, due to important results obtained with proteomics, a great interest …

Scalable steady state analysis of Boolean biological regulatory networks

F Ay, F Xu, T Kahveci - PloS one, 2009 - journals.plos.org
Background Computing the long term behavior of regulatory and signaling networks is
critical in understanding how biological functions take place in organisms. Steady states of …

Pan-genomics: Applications, challenges, and future prospects

D Barh, SC Soares, S Tiwari, VADC Azevedo - 2020 - books.google.com
Pan-genomics: Applications, Challenges, and Future Prospects covers current approaches,
challenges and future prospects of pan-genomics. The book discusses bioinformatics tools …

AlignMCL: Comparative analysis of protein interaction networks through Markov clustering

M Mina, PH Guzzi - 2012 IEEE International Conference on …, 2012 - ieeexplore.ieee.org
Evolutionary analysis and comparison of biological networks may result in the identification
of conserved mechanism between species as well as conserved modules, such as protein …