Related papers: Exploring gene content with pangene graphs
Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical…
Research done using model organisms has been fundamental to the biological understanding of human genes, diseases and phenotypes. Model organisms provide tractable systems for experiments to enhance understanding of biological mechanisms…
Probabilistic biological network growth models have been utilized for many tasks including but not limited to capturing mechanism and dynamics of biological growth activities, null model representation, capturing anomalies, etc. Well-known…
One of the important questions in biological evolution is to know if certain changes along protein coding genes have contributed to the adaptation of species. This problem is known to be biologically complex and computationally very…
The advent of high-throughput sequencing technologies has lead to vast comparative genome sequences. The construction of gene-gene interaction networks or dependence graphs on the genome scale is vital for understanding the regulation of…
The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools…
The pathway is a biological term that refers to a series of interactions between molecules in a cell that causes a certain product or a change in the cell. Pathway analysis is a powerful method for gene expression analysis. Through pathway…
Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis we compare the dynamics of genome evolution in…
Motivation: Histone modifications are among the most important factors that control gene regulation. Computational methods that predict gene expression from histone modification signals are highly desirable for understanding their…
We outline the global control architecture of genomes. A theory of genomic control information is presented. The concept of a developmental control network called a cene (for control gene) is introduced. We distinguish parts-genes from…
DNA rearrangement processes recombine gene segments that are organized on the chromosome in a variety of ways. The segments can overlap, interleave or one may be a subsegment of another. We use directed graphs to represent segment…
Motivation: Bacteriophages (aka phages), which mainly infect bacteria, play key roles in the biology of microbes. As the most abundant biological entities on the planet, the number of discovered phages is only the tip of the iceberg.…
It has been estimated that about 30% of the genes in the human genome are regulated by microRNAs (miRNAs). These are short RNA sequences that can down-regulate the levels of mRNAs or proteins in animals and plants. Genes regulated by miRNAs…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
In biological experiments researchers often have information in the form of a graph that supplements observed numerical data. Incorporating the knowledge contained in these graphs into an analysis of the numerical data is an important and…
The main goal of Systems Biology research is to reconstruct biological networks for its topological analysis so that reconstructed networks can be used for the identification of various kinds of disease. The availability of high-throughput…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
All cells respond to changes in both their internal milieu and the environment around them through the regulation of their genes. Despite decades of effort, there remain huge gaps in our knowledge of both the function of many genes (the…
Increasing evidence has shown that gene-gene interactions have important effects on biological processes of human diseases. Due to the high dimensionality of genetic measurements, existing interaction analysis methods usually suffer from a…
Due to recent breakthroughs in state-of-the-art DNA sequencing technology, genomics data sets have become ubiquitous. The emergence of large-scale data sets provides great opportunities for better understanding of genomics, especially gene…