Gene co-expression network reconstruction: a review on computational methods for inferring functional information from plant-based expression data

A Emamjomeh, E Saboori Robat, J Zahiri… - Plant biotechnology …, 2017 - Springer
Reconstruction of gene co-expression networks is a powerful tool for better understanding of
gene function, biological processes, and complex disease mechanisms. In essence, co …

A guide to gene regulatory network inference for obtaining predictive solutions: Underlying assumptions and fundamental biological and data constraints

S Barbosa, B Niebel, S Wolf, K Mauch, R Takors - Biosystems, 2018 - Elsevier
The study of biological systems at a system level has become a reality due to the increasing
powerful computational approaches able to handle increasingly larger datasets. Uncovering …

GENIRF: An algorithm for gene regulatory network inference using rotation forest

J Pirgazi, AR Khanteymoori… - Current …, 2018 - ingentaconnect.com
Background: A central problem of systems biology is the reconstruction of the topology of
gene regulatory networks (GRNs) using high throughput genomic data like microarray gene …

Review of dimensionality reduction techniques using clustering algorithm in reconstruction of gene regulatory networks

W Pindah, S Nordin, A Seman… - … and Control Technology …, 2015 - ieeexplore.ieee.org
Reconstruction of gene regulatory networks orreverse-engineering'is a process of identifying
gene interaction networks from experimental microarray gene expression profile through …

TIGRNCRN: Trustful inference of gene regulatory network using clustering and refining the network

J Pirgazi, AR Khanteymoori… - Journal of bioinformatics …, 2019 - World Scientific
In this study, in order to deal with the noise and uncertainty in gene expression data,
learning networks, especially Bayesian networks, that have the ability to use prior …

Single-cell regulatory network inference and clustering from high-dimensional sequencing data

AG Vrahatis, GN Dimitrakopoulos… - … Conference on Big …, 2019 - ieeexplore.ieee.org
We are in the big data era which has affected several domains including biomedicine and
healthcare. This revolution driven by the explosion of biomedical data offers the potential for …

From genome-scale data to models of infectious disease: a Bayesian network-based strategy to drive model development

W Yin, JC Kissinger, A Moreno, MR Galinski… - Mathematical …, 2015 - Elsevier
High-throughput, genome-scale data present a unique opportunity to link host to pathogen
on a molecular level. Forging such connections will help drive the development of …

Revisiting bfr clustering algorithm for large scale gene regulatory network reconstruction using mapreduce

M Daoudi, S Meshoul - Proceedings of the 2nd international Conference …, 2017 - dl.acm.org
Inferring gene regulatory network (GRN) is one of the major challenges in bioinformatics. A
great amount of gene expression data is being produced raising the issue of GRN …

Gene regulatory network inference incorporating maximal information coefficient into minimal redundancy network

MAH Akhand, RN Nandi, SM Amran… - 2015 International …, 2015 - ieeexplore.ieee.org
Gene Regulatory Network (GRN) plays an important role to understand the interactions and
dependencies of genes in different conditions from gene expression data. An information …

Reconstruction of gene network through backward elimination based information-theoretic inference with maximal information coefficient

AK Paul, PC Shill - … Conference on Imaging, Vision & Pattern …, 2017 - ieeexplore.ieee.org
For understanding the complex processes of regulation within the system of cellular and
every process of life in different developmental and environmental contexts, reconstructing …