Gene regulatory network inference resources: A practical overview

D Mercatelli, L Scalambra, L Triboli, F Ray… - Biochimica et Biophysica …, 2020 - Elsevier
Transcriptional regulation is a fundamental molecular mechanism involved in almost every
aspect of life, from homeostasis to development, from metabolism to behavior, from reaction …

Combining complex networks and data mining: why and how

M Zanin, D Papo, PA Sousa, E Menasalvas, A Nicchi… - Physics Reports, 2016 - Elsevier
The increasing power of computer technology does not dispense with the need to extract
meaningful information out of data sets of ever growing size, and indeed typically …

Supervised, semi-supervised and unsupervised inference of gene regulatory networks

SR Maetschke, PB Madhamshettiwar… - Briefings in …, 2014 - academic.oup.com
Inference of gene regulatory network from expression data is a challenging task. Many
methods have been developed to this purpose but a comprehensive evaluation that covers …

A feature selection technique for inference of graphs from their known topological properties: Revealing scale-free gene regulatory networks

FM Lopes, DC Martins Jr, J Barrera, RM Cesar Jr - Information Sciences, 2014 - Elsevier
An important problem in bioinformatics is the inference of gene regulatory networks (GRNs)
from expression profiles. In general, the main limitations faced by GRN inference methods …

[PDF][PDF] Information-Theoretic Inference of Gene Networks Using Backward Elimination.

P Meyer, D Marbach, S Roy, M Kellis - BioComp, 2010 - dspace.mit.edu
Unraveling transcriptional regulatory networks is essential for understanding and predicting
cellular responses in different developmental and environmental contexts. Information …

Gene expression complex networks: synthesis, identification, and analysis

FM Lopes, RM Cesar Jr, LDF Costa - Journal of Computational …, 2011 - liebertpub.com
Thanks to recent advances in molecular biology, allied to an ever increasing amount of
experimental data, the functional state of thousands of genes can now be extracted …

[HTML][HTML] Inference of gene regulatory networks from time series by Tsallis entropy

FM Lopes, EA de Oliveira, RM Cesar - BMC systems biology, 2011 - Springer
Background The inference of gene regulatory networks (GRNs) from large-scale expression
profiles is one of the most challenging problems of Systems Biology nowadays. Many …

[HTML][HTML] Gene regulatory networks inference using a multi-GPU exhaustive search algorithm

FF Borelli, RY de Camargo, DC Martins… - BMC …, 2013 - Springer
Background Gene regulatory networks (GRN) inference is an important bioinformatics
problem in which the gene interactions need to be deduced from gene expression data …

Finding Small Consistent Subset for the Nearest Neighbor Classifier Based on Support Graphs

M García-Borroto, Y Villuendas-Rey… - Progress in Pattern …, 2009 - Springer
Finding a minimal subset of objects that correctly classify the training set for the nearest
neighbors classifier has been an active research area in Pattern Recognition and Machine …

Accelerating gene regulatory networks inference through GPU/CUDA programming

FF Borelli, RY Camargo, DC Martins… - 2012 IEEE 2nd …, 2012 - ieeexplore.ieee.org
Gene regulatory networks (GRN) inference is an important bioinformatics problem in which
the gene interactions need to be deduced from gene expression data, such as microarray …