Computational methods for gene regulatory networks reconstruction and analysis: a review

FM Delgado, F Gómez-Vela - Artificial intelligence in medicine, 2019 - Elsevier
In the recent years, the vast amount of genetic information generated by new-generation
approaches, have led to the need of new data handling methods. The integrative analysis of …

The spring of systems biology-driven breeding

J Lavarenne, S Guyomarc'h, C Sallaud, P Gantet… - Trends in plant …, 2018 - cell.com
Genetics and molecular biology have contributed to the development of rationalized plant
breeding programs. Recent developments in both high-throughput experimental analyses of …

Inference of the gene regulatory network acting downstream of CROWN ROOTLESS 1 in rice reveals a regulatory cascade linking genes involved in auxin signaling …

J Lavarenne, M Gonin, S Guyomarc'h… - The Plant …, 2019 - Wiley Online Library
Crown roots (CRs) are essential components of the rice root system. Several genes involved
in CR initiation or development have been identified but our knowledge about how they …

Computational Ensemble Gene Co-Expression Networks for the Analysis of Cancer Biomarkers

J Figueroa-Martínez, DM Saz-Navarro… - Informatics, 2024 - mdpi.com
Gene networks have become a powerful tool for the comprehensive examination of gene
expression patterns. Thanks to these networks generated by means of inference algorithms …

GNC–app: A new Cytoscape app to rate gene networks biological coherence using gene–gene indirect relationships

JJ Díaz-Montaña, F Gómez-Vela, N Díaz-Díaz - Biosystems, 2018 - Elsevier
Motivation Gene networks are currently considered a powerful tool to model biological
processes in the Bioinformatics field. A number of approaches to infer gene networks and …

[HTML][HTML] Gfd-net: A novel semantic similarity methodology for the analysis of gene networks

JJ Díaz-Montaña, N Díaz-Díaz… - Journal of Biomedical …, 2017 - Elsevier
Since the popularization of biological network inference methods, it has become crucial to
create methods to validate the resulting models. Here we present GFD-Net, the first …

Development and use of a Cytoscape app for GRNCOP2

JJ Díaz–Montaña, N Díaz–Díaz, CD Barranco… - Computer Methods and …, 2019 - Elsevier
Abstract Background and Objective: Gene regulatory networks (GRNs) are essential for
understanding most molecular processes. In this context, the so-called model-free …

Crosstalk pathway inference using topological information and biclustering of gene expression data

JS Dussaut, CA Gallo, RL Cecchini, JA Carballido… - Biosystems, 2016 - Elsevier
Detection of crosstalks among pathways is a challenging task, which requires the
identification of different types of interactions associated with cellular processes. A common …