BACKGROUND: Testing predefined gene categories has become a common practice for scientists analyzing high throughput transcriptome data. A systematic way of testing gene categories leads to testing hundreds of null hypotheses that correspond to nodes...
Journal of computational biology : a journal of computational molecular cell biology
30052049
Expression quantitative trait loci (eQTL) analysis is an emerging method for establishing the impact of genetic variations (such as single nucleotide polymorphisms) on the expression levels of genes. Although different methods for evaluating the impa...
Key challenges for human genetics, precision medicine and evolutionary biology include deciphering the regulatory code of gene expression and understanding the transcriptional effects of genome variation. However, this is extremely difficult because ...
To understand the pathophysiology of complex diseases, including hypertension, diabetes, and autism, deleterious phenotypes are unlikely due to the effects of single genes, but rather, gene-gene interactions (GGIs), which are widely analyzed by multi...
The Plant journal : for cell and molecular biology
30500991
Recent advances in genomics technologies have greatly accelerated the progress in both fundamental plant science and applied breeding research. Concurrently, high-throughput plant phenotyping is becoming widely adopted in the plant community, promisi...
Successful development of biological databases requires accommodation of the burgeoning amounts of data from high-throughput genomics pipelines. As the volume of curated data in Animal QTLdb (https://www.animalgenome.org/QTLdb) increases exponentiall...
Genomic prediction benefits hybrid rice breeding by increasing selection intensity and accelerating breeding cycles. With the rapid advancement of technology, other omic data, such as metabolomic data and transcriptomic data, are readily available fo...
Genomic prediction (GP) aims to construct a statistical model for predicting phenotypes using genome-wide markers and is a promising strategy for accelerating molecular plant breeding. However, current progress of phenotype prediction using genomic d...
Genome-wide association studies (GWAS) associate single nucleotide polymorphisms (SNPs) to complex phenotypes. Most human SNPs fall in non-coding regions and are likely regulatory SNPs, but linkage disequilibrium (LD) blocks make it difficult to dist...
Linkage mapping is one of the most commonly used methods to identify genetic loci that determine a trait. However, the loci identified by linkage mapping may contain hundreds of candidate genes and require a time-consuming and labor-intensive fine ma...