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 …

[HTML][HTML] Genomics to systems biology in animal and veterinary sciences: progress, lessons and opportunities

HN Kadarmideen - Livestock Science, 2014 - Elsevier
Livestock genomics has gone through a paradigm shift since the advent of genome
sequencing that includes Genome-Wide Association Studies (GWAS), Whole Genome …

Orchestrating information across tissues via a novel multitask GAT framework to improve quantitative gene regulation relation modeling for survival analysis

M Duan, Y Wang, D Zhao, H Liu, G Zhang… - Briefings in …, 2023 - academic.oup.com
Survival analysis is critical to cancer prognosis estimation. High-throughput technologies
facilitate the increase in the dimension of genic features, but the number of clinical samples …

High-performance computing to detect epistasis in genome scale data sets

A Upton, O Trelles, JA Cornejo-García… - Briefings in …, 2016 - academic.oup.com
It is becoming clear that most human diseases have a complex etiology that cannot be
explained by single nucleotide polymorphisms (SNPs) or simple additive combinations; the …

Co-expression network analysis identifies a gene signature as a predictive biomarker for energy metabolism in osteosarcoma

N Zhu, J Hou, G Ma, S Guo, C Zhao, B Chen - Cancer Cell International, 2020 - Springer
Background Osteosarcoma (OS) is a common malignant bone tumor originating in the
interstitial tissues and occurring mostly in adolescents and young adults. Energy metabolism …

Data integration in poplar:'omics layers and integration strategies

D Weighill, TJ Tschaplinski, GA Tuskan… - Frontiers in …, 2019 - frontiersin.org
Populus trichocarpa is an important biofuel feedstock that has been the target of extensive
research and is emerging as a model organism for plants, especially woody perennials. This …

Genome-wide epistatic interaction networks affecting feed efficiency in duroc and landrace pigs

P Banerjee, VAO Carmelo, HN Kadarmideen - Frontiers in genetics, 2020 - frontiersin.org
Interactions among genomic loci have often been overlooked in genome-wide association
studies, revealing the combinatorial effects of variants on phenotype or disease …

Integrative analysis of genomics and transcriptome data to identify potential functional genes of BMDs in females

YC Chen, YF Guo, H He, X Lin, XF Wang… - Journal of Bone and …, 2016 - academic.oup.com
Osteoporosis is known to be highly heritable. However, to date, the findings from more than
20 genome‐wide association studies (GWASs) have explained less than 6% of genetic …

Prediction of VEGF-C as a key target of pure total flavonoids from citrus against NAFLD in mice via network pharmacology

W Hong, S Li, L Wu, B He, J Jiang… - Frontiers in Pharmacology, 2019 - frontiersin.org
Pure total flavonoids from Citrus (PTFC) effectively reduce the symptoms of non-alcoholic
fatty liver disease (NAFLD). Our previous microarray analysis uncovered the alterations of …

Extensive haplotypes are associated with population differentiation and environmental adaptability in Upland cotton (Gossypium hirsutum)

P Dai, G Sun, Y Jia, Z Pan, Y Tian, Z Peng, H Li… - Theoretical and Applied …, 2020 - Springer
Key message Three extensive eco-haplotypes associated with population differentiation and
environmental adaptability in Upland cotton were identified, with A06_85658585 …