Gene Network: Model, Dynamics and Simulation
AbstractA gene network is modeled as a dynamical random graph whose vertices and edges represent genes and gene-gene interactions, respectively. The network grows through three biological mechanisms:...
View ArticleSplitTester : software to identify domains responsible for functional...
AbstractBackgroundMany protein families have undergone functional divergence after gene duplications such that current subgroups of the family carry out overlapping but distinct biological roles. For...
View ArticleIntron gain and loss in segmentally duplicated genes in rice
AbstractBackgroundIntrons are under less selection pressure than exons, and consequently, intronic sequences have a higher rate of gain and loss than exons. In a number of plant species, a large...
View ArticleMeasuring Spatiotemporal Distortions with GRENOUILLE
AbstractResearchers often implicitly assume in their ultrafast studies that their laser beams have separable spatial and temporal dependencies. This underlying assumption greatly simplifies the...
View ArticleThe General Theory of the First-Order Spatio-Temporal Couplings of Gaussian...
AbstractWe present a general, simple and rigorous theory for the first order spatio-temporal couplings in ultrashort laser pulses. Our model not only identifies all possible couplings, but also yields...
View ArticleFirst-order Spatiotemporal Distortions of Gaussian Pulses and Beams
AbstractUltrashort laser pulses are usually expressed in terms of the temporal and spectral dependencies of their electric field. In this way, it is implicitly assumed that the spatial dependencies of...
View ArticleA bootstrap based analysis pipeline for efficient classification of...
AbstractBackgroundPhylogenetically related miRNAs (miRNA families) convey important information of the function and evolution of miRNAs. Due to the special sequence features of miRNAs, pair-wise...
View ArticleStabilizing selection of protein function and distribution of selection...
AbstractIn this study, I take a new approach to modeling the evolutionary constraint of protein sequence, introducing the stabilizing selection of protein function into the nearly-neutral theory. In...
View ArticleTissue-driven Hypothesis with Gene Ontology (GO) Analysis
AbstractMost of the genes are under selective pressure to maintain their expression levels in the tissues. In a recent study, we have proposed a “tissue-driven” hypothesis stating that the stabilizing...
View ArticleEvolutionary Analysis for Functional Divergence of the Toll-Like Receptor...
AbstractThe Toll-like receptor (TLR) gene family consists of type 1 transmembrane receptors, which play essential roles in both innate immunity and adaptive immune response by ligand recognition and...
View ArticleCharacterization of paralogous protein families in rice
AbstractBackgroundHigh gene numbers in plant genomes reflect polyploidy and major gene duplication events. Oryza sativa, cultivated rice, is a diploid monocotyledonous species with a ~390 Mb genome...
View ArticlePredicting the Proportion of Essential Genes in Mouse Duplicates Based on...
AbstractIn the yeast or nematode, the proportion of essential genes in duplicates is lower than in singletons (single-copy genes), due to the functional redundancy. One may expect that it should be the...
View ArticleDifferences in duplication age distributions between human GPCRs and their...
AbstractBackgroundHow gene duplication has influenced the evolution of gene networks is one of the core problems in evolution. Current duplication-divergence theories generally suggested that genes on...
View ArticleComparative study of human mitochondrial proteome reveals extensive protein...
AbstractBackgroundGene and genome duplication is the principle creative force in evolution. Recently, protein subcellular relocalization, or neolocalization was proposed as one of the mechanisms...
View ArticleComparative analyses reveal distinct sets of lineage-specific genes within...
AbstractBackgroundThe availability of genome and transcriptome sequences for a number of species permits the identification and characterization of conserved as well as divergent genes such as...
View ArticleGenome factor and gene pleiotropy hypotheses in protein evolution
Abstract The debate of genomic correlations between sequence conservation, protein connectivity, gene essentiality and gene expression, has generated a number of new hypotheses that are challenging the...
View ArticleGene Duplication and Functional Consequences
AbstractDue to genome-wide or local chromosome duplication events, in almost all organisms, many genes are represented as several paralogs (duplicate genes) in the genome with related but distinct...
View ArticleNetwork motif comparison rationalizes Sec1/Munc18-SNARE regulation mechanism...
AbstractBackgroundNetwork motifs, recurring subnetwork patterns, provide significant insight into the biological networks which are believed to govern cellular processes.MethodsWe present a comparative...
View ArticleHistone modification pattern evolution after yeast gene duplication
AbstractBackgroundGene duplication and subsequent functional divergence especially expression divergence have been widely considered as main sources for evolutionary innovations. Many studies evidenced...
View ArticleAge distribution patterns of human gene families: divergent for Gene Ontology...
AbstractThe age distribution of gene duplication events within the human genome exhibits two waves of duplications along with an ancient component. However, because of functional constraint...
View Article
