Meta-research: evaluation and improvement of research methods and practices

JPA Ioannidis, D Fanelli, DD Dunne, SN Goodman - PLoS biology, 2015 - journals.plos.org
As the scientific enterprise has grown in size and diversity, we need empirical evidence on
the research process to test and apply interventions that make it more efficient and its results …

Revisiting date and party hubs: novel approaches to role assignment in protein interaction networks

S Agarwal, CM Deane, MA Porter… - PLoS computational …, 2010 - journals.plos.org
The idea of “date” and “party” hubs has been influential in the study of protein–protein
interaction networks. Date hubs display low co-expression with their partners, whilst party …

Modular pharmacology: deciphering the interacting structural organization of the targeted networks

Z Wang, Y Wang - Drug discovery today, 2013 - Elsevier
Because multiple drugs act within the context of the regulatory networks in which drug
targets and disease gene products function, module-designed studies are becoming …

A semi-supervised fuzzy clustering algorithm applied to gene expression data

IA Maraziotis - Pattern Recognition, 2012 - Elsevier
Over the last decade there has been an increasing interest in semi-supervised clustering.
Several studies have suggested that even a small amount of supervised information can …

Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis

J Gu, Y Chen, S Li, Y Li - BMC systems biology, 2010 - Springer
Background Cell responses to environmental stimuli are usually organized as relatively
separate responsive gene modules at the molecular level. Identification of responsive gene …

Investigation of hypoxia networks in ovarian cancer via bioinformatics analysis

K Zhang, X Kong, G Feng, W Xiang, L Chen… - Journal of ovarian …, 2018 - Springer
Background Ovarian cancer is a leading cause of the death from gynecologic malignancies.
Hypoxia is closely related to the malignant growth of cells. However, the molecular …

MicroRNA expression analysis: clinical advantage of propranolol reveals key microRNAs in myocardial infarction

W Zhu, L Yang, H Shan, Y Zhang, R Zhou, Z Su, Z Du - PLoS One, 2011 - journals.plos.org
Background As playing important roles in gene regulation, microRNAs (miRNAs) are
believed as indispensable involvers in the pathogenesis of myocardial infarction (MI) that …

Identify bilayer modules via pseudo-3D clustering: applications to miRNA-gene bilayer networks

Y Xu, M Guo, X Liu, C Wang, Y Liu… - Nucleic acids research, 2016 - academic.oup.com
Module identification is a frequently used approach for mining local structures with more
significance in global networks. Recently, a wide variety of bilayer networks are emerging to …

Bioinformatics analysis of the molecular mechanism of diffuse intrinsic pontine glioma

L Deng, P Xiong, Y Luo, X Bu, S Qian… - Oncology …, 2016 - spandidos-publications.com
The present study aimed to elucidate key molecular mechanisms in the progression of
diffuse intrinsic pontine glioma (DIPG). The gene expression profile GSE50021, which …

Biological mechanisms of growth performance and meat quality in porcine muscle tissue

C Fang, F Guo, X Zhao, Z Zhang, J Lu, H Pan… - Animal …, 2022 - Taylor & Francis
Growth performance and meat quality are important traits for pig production. The aim of the
present study was to investigate the molecular mechanisms underlying growth performance …