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A gene network inference method from continuous-value gene expression data of wild-type and mutants.
In this paper, we introduce a new inference method of a gene regulatory network from steady-state gene expression data. Expand
Simulation of Genetic Interaction for Drosophila Leg Formation
  • K. Kyoda, H. Kitano
  • Biology, Computer Science
  • Pacific Symposium on Biocomputing
  • 1 December 1998
In this paper, we present a simulation system for leg formation, simulating the genes interactions involved in establishing three principal axes (A-P, D-V, and P-D) of leg formation. Expand
WDDD: Worm Developmental Dynamics Database
We created a database, the Worm Developmental Dynamics Database (http://so.riken.jp/wddd/), 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
We have developed the Systems Science of Biological Dynamics database (SSBD) to store and share quantitative biological dynamics data. Expand
The DBRF Method for Inferring a Gene Network from Large-scale Steady-state Gene Expression Data
genome sequence has enabled whole-genome expression profiling and genome deletion projects, which are generating large-scale gene expression profiles corresponding to hundreds of deletion mutants. ToExpand
Construction of a generalized simulator for multi-cellular organisms and its application to SMAD signal transduction.
In this paper, we report development of a generalized simulation system based on ordinary differential equations for multi-cellular organisms, and results of the analysis on a Smad signalExpand
DBRF-MEGN method: an algorithm for deducing minimum equivalent gene networks from large-scale gene expression profiles of gene deletion mutants
We developed 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. Expand
Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data
Biological Dynamics Markup Language is an open XML-based format for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. Expand
A Model of Axis Determination for the Drosophila Wing Disc
In this paper we propose a comprehensive model of axis determination for the Drosophila wing disc, and we simulate spatio-temporal gene expression patterning in the wing disc. Expand
Development of an Integrated Visualization System for Phenotypic Character Networks
We present an integrated visualization system for a causality network constructed from phenotypic developmental characters and their related scientific literature. Expand