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 …

A survey of computational intelligence techniques in protein function prediction

AK Tiwari, R Srivastava - International journal of proteomics, 2014 - Wiley Online Library
During the past, there was a massive growth of knowledge of unknown proteins with the
advancement of high throughput microarray technologies. Protein function prediction is the …

DeepFunc: a deep learning framework for accurate prediction of protein functions from protein sequences and interactions

F Zhang, H Song, M Zeng, Y Li, L Kurgan, M Li - Proteomics, 2019 - Wiley Online Library
Annotation of protein functions plays an important role in understanding life at the molecular
level. High‐throughput sequencing produces massive numbers of raw proteins sequences …

Phenotypic Analyses of Arabidopsis T-DNA Insertion Lines and Expression Profiling Reveal That Multiple L-Type Lectin Receptor Kinases Are Involved in Plant …

Y Wang, K Bouwmeester, P Beseh… - Molecular Plant …, 2014 - Am Phytopath Society
L-type lectin receptor kinases (LecRK) are membrane-spanning receptor-like kinases with
putative roles in biotic and abiotic stress responses and in plant development. In …

Detecting temporal protein complexes from dynamic protein-protein interaction networks

L Ou-Yang, DQ Dai, XL Li, M Wu, XF Zhang, P Yang - BMC bioinformatics, 2014 - Springer
Background Proteins dynamically interact with each other to perform their biological
functions. The dynamic operations of protein interaction networks (PPI) are also reflected in …

Si-CSP9 regulates the integument and moulting process of larvae in the red imported fire ant, Solenopsis invicta

D Cheng, Y Lu, L Zeng, G Liang, X He - Scientific Reports, 2015 - nature.com
Chemosensory proteins (CSPs) have been predicted to be involved in development;
however, direct evidence for their involvement is lacking and genetic basis is largely …

Nonnegative principal component analysis for cancer molecular pattern discovery

X Han - IEEE/ACM Transactions on Computational Biology and …, 2009 - ieeexplore.ieee.org
As a well-established feature selection algorithm, principal component analysis (PCA) is
often combined with the state-of-the-art classification algorithms to identify cancer molecular …

A new unsupervised gene clustering algorithm based on the integration of biological knowledge into expression data

M Verbanck, S Lê, J Pagès - BMC bioinformatics, 2013 - Springer
Background Gene clustering algorithms are massively used by biologists when analysing
omics data. Classical gene clustering strategies are based on the use of expression data …

Reconstruction of the protein-protein interaction network for protein complexes identification by walking on the protein pair fingerprints similarity network

B Xu, Y Liu, C Lin, J Dong, X Liu, Z He - Frontiers in genetics, 2018 - frontiersin.org
Identifying protein complexes from protein-protein interaction networks (PPINs) is important
to understand the science of cellular organization and function. However, PPINs produced …

The impact of protein interaction networks' characteristics on computational complex detection methods

X Liu, Z Yang, Z Zhou, Y Sun, H Lin, J Wang… - Journal of theoretical …, 2018 - Elsevier
Protein complexes of physically interacting proteins play an important role in organizing
various biological processes in the cell. Therefore, correctly identifying complexes is useful …