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A gene network inference method from continuous-value gene expression data of wild-type and mutants.
TLDR
A new inference method of a gene regulatory network from steady-state gene expression data is introduced, which shows the superiority of using continuous values to binary values and is compared with that of predictor method proposed by Ideker et al. Expand
Simulation of Genetic Interaction for Drosophila Leg Formation
  • K. Kyoda, H. Kitano
  • Biology, Computer Science
  • Pacific Symposium on Biocomputing
  • 1 December 1998
TLDR
The so-called Bi-Polar Model describes axial formation of the leg disc well and suggests that P-D axis can be formed by a set of genes with different activation thresholds, forming a bi-polar contour. Expand
WDDD: Worm Developmental Dynamics Database
TLDR
A database, the Worm Developmental Dynamics Database, is created, which stores a collection of quantitative information about cell division dynamics in early Caenorhabditis elegans embryos with single genes silenced by RNA-mediated interference. Expand
SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena
TLDR
The Systems Science of Biological Dynamics database (SSBD) is developed to store and share quantitative biological dynamics data for single molecules, nuclei and whole organisms in a wide variety of model organisms. Expand
The DBRF Method for Inferring a Gene Network from Large-scale Steady-state Gene Expression Data
TLDR
The Difference-Based Regulation Finding (DBRF) method, which infers the underlying gene network from those profiles corresponding to hundreds of deletion mutants, and shows that the performance of the DBRF method is superior to that of the predictor method. Expand
Construction of a generalized simulator for multi-cellular organisms and its application to SMAD signal transduction.
TLDR
A generalized simulation system based on ordinary differential equations for multi-cellular organisms, and results of the analysis on a Smad signal transduction cascade suggest that the presence of negative feedback mechanism in the Smad pathway functions to improve the frequency response of the cascade against changes in the signaling. Expand
DBRF-MEGN method: an algorithm for deducing minimum equivalent gene networks from large-scale gene expression profiles of gene deletion mutants
TLDR
The DBRF-MEGN (difference-based regulation finding-minimum equivalent gene network) method, in which an algorithm deduces the most parsimonious SDGs consistent with expression profiles of gene deletion mutants, is developed and confirmed. Expand
Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data
TLDR
An open unified format, Biological Dynamics Markup Language (BDML), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms and will improve the efficiency of development and evaluation of software tools for data visualization and analysis. Expand
A Model of Axis Determination for the Drosophila Wing Disc
TLDR
A comprehensive model of axis determination for the Drosophila wing disc is proposed, and the role of interaction among several genes involved has been analyzed systematically and the results illustrate that successful reconstruction of the gene expression patterns observed in the actual wing disc requires several hypothetical gene regulations. Expand
Development of an Integrated Visualization System for Phenotypic Character Networks
TLDR
This work presents an integrated visualization system for a causality network constructed from phenotypic developmental characters and their related scientific literature, which provides both explanatory and verification visualization functions. Expand
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