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Alternative splicing is a ubiquitous gene regulatory mechanism that dramatically increases the complexity of the proteome. In this paper we study splicing module, which we define as a set of cassette exons co-regulated by the same splicing factors. We have designed a tensor-based approach to identify co-splicing clusters that appear frequently across multiple conditions, thus very likely to represent...
With the development of high-throughput technologies, e.g. microarrays and the second generation sequencing technologies, gene expression profiles have been applied widely to characterize the functional states of various samples at different conditions. This is especially important for clinical biomarker identification that is vital to the understanding of the pathogenesis of a certain disease and...
Gene regulation is a key factor in gaining a full understanding of molecular biology. microRNA (miRNA), a novel class of non-coding RNA, has recently been found to be one crucial class of post-transactional regulators, and play important parts in cancer. One essential step to understand the regulatory effect of miRNAs is the reliable prediction of their target mRNAs. Typically, the predictions are...
Mathematical models have been used to understand the factors that govern infectious disease progression in viral infections. Two basic models of within-host viral infection, proposed by Nowak et. al. and Perelson et. al. respectively, have been widely used in the studies of HBV and HIV infections. However, the loss term of viral particles when it enters the target cells are both ignored by these two...
We studied the floral morphology and floral biology of Cynanchum otophyllum Schneid in experimental plots and field sites. Some observations were augmented by laboratory studies of floral traits, including scanning electron microscopy and light microscopy. The flower was characterized by a staminal corona. The pollinia were lodged in sacs on each side of the stigma and needed pollen vector for fruit...
Recently, we have identified 39 candidates of active regulatory networks for the diabetes progression in Goto-Kakizaki (GK) rat by using the network screening, which were well consistent with the previous knowledge of regulatory relationship between transcription factors (TFs) and their regulated genes. In addition, we have developed a computational procedure for identifying transcriptional master...
Modeling genetic regulatory networks is an important research issue in systems biology. Many mathematical models have been proposed, and among these models, Boolean Network (BN) and its extension Probabilistic Boolean Network (PBN) are popular. In this paper we consider the problem constructing PBNs with gene perturbations. We propose a modified Newton's method to get the gene perturbation probability...
Previously, we developed a biochemical reaction simulator called WinBEST-KIT (Biochemical Engineering System analyzing Tool-KIT, which runs under Microsoft Windows) for analyzing complicated metabolic pathways. WinBEST-KIT provides an integrated simulation environment for experimental researchers in metabolic engineering. A particularly notable feature of WinBEST-KIT is that users can easily define...
Microglia play a pivotal role in synaptic plasticity of chronic pain. In this study, the potential role of interleukin 1beta (IL-1β), mainly released by microglia in early stage of nerve injury, in mechanical allodynia induced by tetanic stimulation of the sciatic nerve (TSS) was examined. Mechanical allodynia was observed on both ipsilateral and contralateral sides of TSS. Moreover, the expression...
Homologous recombination is a fundamental cellular process that is most widely used by cells to rearrange genes and accurately repair DNA double-strand breaks. It may result in the formation of a critical intermediate named Holliday junction, which is a four-way DNA junction and needs to be resolved to allow chromosome segregation. Different Holliday junction resolution systems and enzymes have been...
A general shape equation for the local regular structure of biomolecular chains at the equilibrium state is established. It predicts a general relationship between the structural curvature and torsion, which only concerns about the elastic property of the molecular chain, and is independent of variable conformations of real biomolecules. Solutions corresponding to α-helix and β-hairpin in proteins,...
Identifying corresponding genes (orthologs) in different species is an important step in genome-wide comparative analysis. In particular, one-to-one correspondences between genes in different species greatly simplify certain problems such as transfer of function annotation and genome rearrangement studies. Positional homologs are the direct descendants of a single ancestral gene in the most recent...
The signal peptide of eosinophil cationic protein (ECPsp) is known to play an important role in translocating ECP to extracellular space. However, we previously discovered that ECPsp has a novel function of inhibiting microbial growth and regulating the gene expression of tumor growth factor-alpha (TGF-α) and epidermal growth factor receptor (EGFR) in mammalian cells. In the present study, we first...
The roles of time delay on gene switch and stochastic resonance are systematically explored based on a famous gene transcriptional regulatory model with noises. Our theoretical results show that the time delay can induce the switch, i.e., the TF-A monomer concentration shifts from the high concentration state to the low concentration state (“on”→“off”), and can further accelerate the transition from...
RNA-Seq has become one of the most important new approaches for gene expression analysis as well as transcriptome analysis. The issue of how to analysis RNA-Seq data is one of the biggest challenges for current transcriptomics research. In this study, we develop an RNA-Seq data annotation pipeline named RNADAP, which is an efficient transcriptomes analysis tool to evaluate gene expression quantization...
In general, molecular signatures of diseases are estimated by comparing the two sets of molecular data measured for the samples with distinctive phenotypes, and then molecular functions of the diseases are characterized by the following analyses of the signatures. Unfortunately, ambiguous relationships between molecular signatures and functions are observed in some cases, due to a posteriori justification...
Biology image is a main approach of biology research, So the measurement and recognition accurately of biology image, especially the monometer image like cell image, is very important and critical. All these depend on the accurate display of biology image. A key model of standard display function(SDF) for biology image is established at cell level, and measurement images are calibrated by the metrology...
K-means algorithm is one of the most classic partition algorithms in clustering algorithms. The result obtained by K-means algorithm varies with the choice of the initial clustering centers. Motivated by this, an improved K-means algorithm is proposed based on the Kruskal algorithm, which is famous in graph theory. The procedure of this algorithm is shown as follows: Firstly, the minimum spanning...
Identifying dysregulation modules for complex diseases, such as B-cell lymphomas, can provide insights into the mechanisms of diseases and help to identify novel drug targets. In this work, based on molecular interaction network, we applied a network flow model to identify the dysregulation modules for three subtypes of non-Hodgkin's lymphomas, including Burkitt's lymphoma (BL), follicular lymphoma...
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