As the result of early specification processes, sea urchin embryos eventually form various mesodermal cell lineages and a gut consisting of fore-, mid- and hindgut. The progression of specification as well as the overall spatial organization of the organism is encoded in its gene regulatory networks (GRNs). We have analyzed the GRN driving endoderm specification up to the onset of gastrulation ...

Reconstructing gene regulatory network (GRN) from timeseries expression data has become increasingly popular since time course data contain temporal information about gene regulation. A typical microarray gene expression data contain expressions of thousands of genes but the number of time samples is usually very small. Therefore, inferring a GRN from such a high-dimensional expression data pos...

User’s sensitive image to products is the emphasis that industrial design concerns, and is also the one of the key targets. Complicated mapping relations exist between design elements and user image, which make product’s user image unpredictable. The paper tries to build a model to describe the mapping relations on the basis of graph theory, which introduces the concept of genetic regulatory ne...

VIDEO ABSTRACT The most common inherited form of Frontotemporal Lobar Degeneration (FTLD) known stems from Progranulin (GRN) mutation and exhibits TDP-43 plus ubiquitin aggregates. Despite the causative role of GRN haploinsufficiency in FTLD-TDP, the neurobiology of this secreted glycoprotein is unclear. Here, we examined PGRN binding to the cell surface. PGRN binds to cortical neurons via its ...

Many inference methods have been proposed to reconstruct unknown Gene Regulatory Networks (GRN) using microarray datasets. State Space Model (SSM) is a method that can be used to infer GRNs from a time series dataset. However, there exist two difficulties in SSM when it is applied for GRN reconstruction: how to estimate initial values of parameters and how to learn the genegene interactions in ...

Reverse engineering gene regulatory networks (GRNs), also known as network inference, refers to the process of reconstructing GRNs from gene expression data. Biologists model a GRN as a directed graph in which nodes represent genes and links show regulatory relationships between the genes. By predicting the links to infer a GRN, biologists can gain a better understanding of regulatory circuits ...

Gene Ontology (GO) provides a controlled vocabulary and hierarchy of terms to facilitate the annotation of gene functions and molecular attributes. Given a set of genes, a Gene Ontology Network (GON) can be constructed from the corresponding GO annotations and semantic relations among GO terms. Transitive rules can be applied to GO semantic relations to infer transitive regulations among genes....

Organisms have a remarkable capacity to respond to environmental change. They can either respond directly, by means of phenotypic plasticity, or they can slowly adapt through evolution. Yet, how phenotypic plasticity links to evolutionary adaptability is largely unknown. Current studies of plasticity tend to adopt a phenomenological reaction norm (RN) approach, which neglects the mechanisms und...

OBJECTIVE Frontotemporal dementia (FTD) is characterized by behavioral disturbances and language problems. Familial forms can be caused by genetic defects in microtubule-associated protein tau (MAPT), progranulin (GRN), and C9orf72. In light of upcoming clinical trials with potential disease-modifying agents, the development of sensitive biomarkers to evaluate such agents in the earliest stage ...