Multi-omic data integration and analysis using systems genomics approaches: methods and applications in animal production, health and welfare

P Suravajhala, LJA Kogelman… - Genetics Selection …, 2016 - Springer
In the past years, there has been a remarkable development of high-throughput omics (HTO)
technologies such as genomics, epigenomics, transcriptomics, proteomics and …

[PDF][PDF] Bioinformatics: an overview and its applications

WJS Diniz, F Canduri - Genet Mol Res, 2017 - funpecrp.com.br
Technological advancements in recent years have promoted a marked progress in
understanding the genetic basis of phenotypes. In line with these advances, genomics has …

Gene co-expression analysis for functional classification and gene–disease predictions

S Van Dam, U Vosa, A van der Graaf… - Briefings in …, 2018 - academic.oup.com
Gene co-expression networks can be used to associate genes of unknown function with
biological processes, to prioritize candidate disease genes or to discern transcriptional …

Transcriptome analysis of an apple (Malus × domestica) yellow fruit somatic mutation identifies a gene network module highly associated with anthocyanin and …

I El-Sharkawy, D Liang, K Xu - Journal of experimental botany, 2015 - academic.oup.com
Using RNA-seq, this study analysed an apple (Malus× domestica) anthocyanin-deficient
yellow-skin somatic mutant 'Blondee'(BLO) and its red-skin parent 'Kidd's D-8'(KID), the …

Liver transcriptomic networks reveal main biological processes associated with feed efficiency in beef cattle

PA Alexandre, LJA Kogelman, MHA Santana… - BMC genomics, 2015 - Springer
Background The selection of beef cattle for feed efficiency (FE) traits is very important not
only for productive and economic efficiency but also for reduced environmental impact of …

Comparison of methods for differential co-expression analysis for disease biomarker prediction

T Kakati, DK Bhattacharyya, P Barah… - Computers in biology and …, 2019 - Elsevier
In the recent past, a number of methods have been developed for analysis of biological data.
Among these methods, gene co-expression networks have the ability to mine functionally …

RNA-Seq transcriptomics and pathway analyses reveal potential regulatory genes and molecular mechanisms in high-and low-residual feed intake in Nordic dairy …

MS Salleh, G Mazzoni, JK Höglund, DW Olijhoek… - BMC genomics, 2017 - Springer
Background The selective breeding of cattle with high-feed efficiencies (FE) is an important
goal of beef and dairy cattle producers. Global gene expression patterns in relevant tissues …

Fourth report on chicken genes and chromosomes 2022

J Smith, JM Alfieri, N Anthony, P Arensburger… - … and genome research, 2023 - karger.com
The chicken continues to hold its position as a leading model organism within many areas of
research, as well as being a major source of protein for human consumption. The First …

Identification of a putative quantitative trait nucleotide in guanylate binding protein 5 for host response to PRRS virus infection

JE Koltes, E Fritz-Waters, CJ Eisley, I Choi, H Bao… - BMC genomics, 2015 - Springer
Background Previously, we identified a major quantitative trait locus (QTL) for host response
to Porcine Respiratory and Reproductive Syndrome virus (PRRSV) infection in high linkage …

Genetic architecture and selection of Anhui autochthonous pig population revealed by whole genome resequencing

W Zhang, X Li, Y Jiang, M Zhou, L Liu, S Su, C Xu… - Frontiers in …, 2022 - frontiersin.org
The genetic resources among pigs in Anhui Province are diverse, but their value and
potential have yet to be discovered. To illustrate the genetic diversity and population …