Predicting essential proteins based on weighted degree centrality

X Tang, J Wang, J Zhong, Y Pan - IEEE/ACM Transactions on …, 2013 - ieeexplore.ieee.org
Essential proteins are vital for an organism's viability under a variety of conditions. There are
many experimental and computational methods developed to identify essential proteins …

Computational analysis of protein interaction networks for infectious diseases

A Pan, C Lahiri, A Rajendiran… - Briefings in …, 2016 - academic.oup.com
Infectious diseases caused by pathogens, including viruses, bacteria and parasites, pose a
serious threat to human health worldwide. Frequent changes in the pattern of infection …

On position-specific scoring matrix for protein function prediction

J cheol Jeong, X Lin, XW Chen - IEEE/ACM transactions on …, 2010 - ieeexplore.ieee.org
While genome sequencing projects have generated tremendous amounts of protein
sequence data for a vast number of genomes, substantial portions of most genomes are still …

[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 …

Predicting essential proteins based on RNA-Seq, subcellular localization and GO annotation datasets

X Lei, J Zhao, H Fujita, A Zhang - Knowledge-Based Systems, 2018 - Elsevier
Essential proteins are indispensable to cellular life. Identification of essential proteins plays
a critical role in the survival and development of life process and understanding the function …

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 …

A cross-species study of PI3K protein-protein interactions reveals the direct interaction of P85 and SHP2

SB Breitkopf, X Yang, MJ Begley, M Kulkarni… - Scientific reports, 2016 - nature.com
Using a series of immunoprecipitation (IP)–tandem mass spectrometry (LC-MS/MS)
experiments and reciprocal BLAST, we conducted a fly-human cross-species comparison of …

A protein domain co-occurrence network approach for predicting protein function and inferring species phylogeny

Z Wang, XC Zhang, MH Le, D Xu, G Stacey, J Cheng - PloS one, 2011 - journals.plos.org
Protein Domain Co-occurrence Network (DCN) is a biological network that has not been
fully-studied. We analyzed the properties of the DCNs of H. sapiens, S. cerevisiae, C …

Mr. KNN: soft relevance for multi-label classification

X Lin, X Chen - Proceedings of the 19th ACM international conference …, 2010 - dl.acm.org
Multi-label classification refers to learning tasks with each instance belonging to one or more
classes simultaneously. It arose from real-world applications such as information retrieval …

Revealing and avoiding bias in semantic similarity scores for protein pairs

J Wang, X Zhou, J Zhu, C Zhou, Z Guo - BMC bioinformatics, 2010 - Springer
Background Semantic similarity scores for protein pairs are widely applied in functional
genomic researches for finding functional clusters of proteins, predicting protein functions …