Recurrent neural network based hybrid model for reconstructing gene regulatory network

K Raza, M Alam - Computational biology and chemistry, 2016 - Elsevier
One of the exciting problems in systems biology research is to decipher how genome
controls the development of complex biological system. The gene regulatory networks …

Neural model of gene regulatory network: a survey on supportive meta-heuristics

S Biswas, S Acharyya - Theory in Biosciences, 2016 - Springer
Gene regulatory network (GRN) is produced as a result of regulatory interactions between
different genes through their coded proteins in cellular context. Having immense importance …

A Bi-objective RNN model to reconstruct gene regulatory network: a modified multi-objective simulated annealing approach

S Biswas, S Acharyya - IEEE/ACM Transactions on …, 2017 - ieeexplore.ieee.org
Gene Regulatory Network (GRN) is a virtual network in a cellular context of an organism,
comprising a set of genes and their internal relationships to regulate protein production rate …

[HTML][HTML] A robust gene regulatory network inference method base on Kalman filter and linear regression

J Pirgazi, AR Khanteymoori - PloS one, 2018 - journals.plos.org
The reconstruction of the topology of gene regulatory networks (GRNs) using high
throughput genomic data such as microarray gene expression data is an important problem …

Construction of gene regulatory networks using recurrent neural networks and swarm intelligence

A Khan, S Mandal, RK Pal, G Saha - Scientifica, 2016 - Wiley Online Library
We have proposed a methodology for the reverse engineering of biologically plausible gene
regulatory networks from temporal genetic expression data. We have used established …

[HTML][HTML] Reverse engineering gene regulatory networks from measurement with missing values

OE Ogundijo, A Elmas, X Wang - EURASIP Journal on Bioinformatics and …, 2016 - Springer
Background Gene expression time series data are usually in the form of high-dimensional
arrays. Unfortunately, the data may sometimes contain missing values: for either the …

[PDF][PDF] Reconstruction of gene regulatory networks from gene expression data using decoupled recurrent neural network model

N Noman, L Palafox, H Iba - Natural computing and beyond, 2013 - library.oapen.org
In this work we used the decoupled version of the recurrent neural network (RNN) model for
gene network inference from gene expression data. In the decoupled version, the global …

A comprehensive overview and critical evaluation of gene regulatory network inference technologies

M Zhao, W He, J Tang, Q Zou… - Briefings in bioinformatics, 2021 - academic.oup.com
Gene regulatory network (GRN) is the important mechanism of maintaining life process,
controlling biochemical reaction and regulating compound level, which plays an important …

[HTML][HTML] Identifying time-delayed gene regulatory networks via an evolvable hierarchical recurrent neural network

MM Kordmahalleh, MG Sefidmazgi, SH Harrison… - BioData mining, 2017 - Springer
Background The modeling of genetic interactions within a cell is crucial for a basic
understanding of physiology and for applied areas such as drug design. Interactions in gene …

Reconstructing gene regulatory networks from knock-out data using Gaussian Noise Model and Pearson Correlation Coefficient

FHM Salleh, SM Arif, S Zainudin… - … biology and chemistry, 2015 - Elsevier
A gene regulatory network (GRN) is a large and complex network consisting of interacting
elements that, over time, affect each other's state. The dynamics of complex gene regulatory …