Search Results for "gene regulatory networks"

TSMiner is a software program for reconstructing time-specific regulatory networks for time-series expression data. TSMiner has three key modules: first, predicting the time-specific activated/repressed transcription factors (TFs); second, predicting the biological pathways associated with the predicted TFs; third, merging the TFs and pathways into time-specific regulatory networks. TSMiner provides extensive interactive operations to help users explore the results of each module. For example...

Although protein-protein interaction networks are an ubiquitous component of modern systems biology, comparatively few efforts have been made to tailor their topology to the actual cellular condition under study. Since a simple reduction of the networks to the subset of expressed genes only scratches the surface of higher organisms’ regulatory capabilities, we propose the advanced method PPIXpress that allows to exploit expression data at the transcript-level and is thus able to also reveal...

Eukaryotic gene expression is controlled through molecular logic circuits that combine regulatory signals of many different factors. Complexation of transcription factors and other regulatory proteins is a prevailing and highly conserved mechanism of signal integration within critical regulatory pathways and enable to infer controlled genes as well as the exerted regulatory mechanism. We developed DACO (domain-aware cohesiveness optimization), a novel algorithm that combines protein-protein...

OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets.

STON, Sbgn TO Neo4j, is a Java-based framework that imports and translates metabolic, signalling and gene regulatory pathways presented in SBGN (Systems Biology Graphical Notation, http://www.sbgn.org) Process Description (PD) and Activity Flow (AF) languages to a graph-oriented format compatible with Neo4j (http://neo4j.com/). STON1.2 allows also to link common processes between two different PD maps. This framework uses two sets of libraries: LibSBGN and Neo4j libraries...

Chromatin accessibility plays a key role in epigenetic regulation of gene activation and silencing. Open chromatin regions allow regulatory elements such as transcription factors and polymerases to bind for gene expression while closed chromatin regions prevent the activity of transcriptional machinery. Recently, nucleosome occupancy and methylome sequencing (NOMe-seq) has been developed for simultaneously profiling of chromatin accessibility and DNA methylation on single molecules. However...

Workbench for visualizing biological networks (regulatory, interaction, and metabolic). Can be used as a front-end for BNDB datawarehouses, but also as stand-alone tool.

GenoCAD is a CAD software for synthetic biology. This application provides a web-based tool to design plasmids, artificial gene networks, and other synthetic genetic systems composed of standard genetic parts. It includes a parts management system, a rule-based design tool, and a simulation engine. This project has morphed into a SaaS model. The open source code is no longer maintained.

Research Article: http://www.sciencedirect.com/science/article/pii/S0898122108006287

GeneNetWeaver (GNW) is an open-source tool for in silico benchmark generation and performance profiling of network inference methods. GNW was used to generate the community-wide DREAM3, DREAM4 and DREAM5 In Silico Challenges.

GRaPe - a platform-independent software tool for building integrative gene-reaction-protein (GRP) networks. It generates the kinetic equations for each reaction and outputs a SBML document. It also implements two methods for parameter estimation.

Genome Data Visualization Toolkit (GDVTK) is a Java library for building bioinformatics visualization application. See Bioinformatics, 2004 Mar 22;20(5):727-34. Java-based application framework for visualization of gene regulatory region annotations.

A simple Java application for the analysis and identification of gene networks. ProPesca takes as input shorts temporal series of realtime-PCR expression levels and it clusters genes that exhibit either similar or specular behaviors.

NetAtlas is a Cytoscape plugin that uses tissue gene expression data to filter cellular signaling network. The plugin identifies of tissue-defined networks, tissue-specific network components, and components with correlated expression across tissues.

Osprey is a software platform for visualization of complex interaction networks. Osprey builds data-rich graphical represetations from Gene Ontology (GO) annotated interactions maintained by the BioGRID.

GeNetDB, contraction of Genetic Network Database, is a bioinformatic platform destined to the study of genetic regulatory networks. It contains in one place the data and the way to study them, providing the user an access to all tools needed for his work