BioNetwork Bench: Database and Software for Storage, Query, and Analysis of Gene and Protein Networks.

scientific article published on 8 November 2012

BioNetwork Bench: Database and Software for Storage, Query, and Analysis of Gene and Protein Networks. is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.4137/BBI.S9728
P932PMC publication ID3498971

P50authorVasant HonavarQ7916327
P2093author name stringFadi Towfic
M. Heather West Greenlee
Oksana Kohutyuk
P2860cites workGenomic analysis of mouse retinal developmentQ21146415
ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular ContextQ21284234
Gene ontology: tool for the unification of biologyQ23781406
Cytoscape: a software environment for integrated models of biomolecular interaction networksQ24515682
KEGG for linking genomes to life and the environmentQ24650347
Osprey: a network visualization systemQ24791459
PathSys: integrating molecular interaction graphs for systems biology.Q25257136
BIOZON: a hub of heterogeneous biological dataQ25257166
pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer.Q25257839
The Gene Ontology (GO) database and informatics resourceQ27860988
Crx, a novel Otx-like paired-homeodomain protein, binds to and transactivates photoreceptor cell-specific genesQ28255968
Graph-based analysis and visualization of experimental results with ONDEXQ28301712
Otx2 homeobox gene controls retinal photoreceptor cell fate and pineal gland developmentQ28505275
Distinct developmental programs require different levels of Bmp signaling during mouse retinal developmentQ28587132
Nrl is required for rod photoreceptor developmentQ28595099
Lethality and centrality in protein networksQ29547267
Network motifs: simple building blocks of complex networksQ29547340
BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networksQ29547427
The large-scale organization of metabolic networksQ29547498
Hierarchical organization of modularity in metabolic networksQ29618451
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression dataQ29618517
Reverse engineering of regulatory networks in human B cellsQ30004211
geWorkbench: an open source platform for integrative genomicsQ30389806
GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway dataQ30912193
Informative structure priors: joint learning of dynamic regulatory networks from multiple types of data.Q30984562
BIOZON: a system for unification, management and analysis of heterogeneous biological dataQ31032436
Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE.Q31050056
Photoreceptor-specific nuclear receptor NR2E3 functions as a transcriptional activator in rod photoreceptorsQ33203655
BioWarehouse: a bioinformatics database warehouse toolkitQ33237374
BiologicalNetworks: visualization and analysis tool for systems biologyQ33250341
Functional clustering of yeast proteins from the protein-protein interaction networkQ33251561
A biphasic pattern of gene expression during mouse retina developmentQ33260567
cPath: open source software for collecting, storing, and querying biological pathwaysQ33263441
ArrayExpress--a public database of microarray experiments and gene expression profilesQ33264889
GenMAPP 2: new features and resources for pathway analysisQ33288654
Targeting of GFP to newborn rods by Nrl promoter and temporal expression profiling of flow-sorted photoreceptorsQ34410806
Modeling and simulation of genetic regulatory systems: a literature reviewQ34575847
The nature of systems biologyQ34582744
The mouse Gene Expression Database (GXD): 2007 updateQ35253029
Integrating 'omic' information: a bridge between genomics and systems biologyQ35556187
From functional genomics to systems biology: concepts and practicesQ35638937
Systems biology, integrative biology, predictive biologyQ36134064
Modeling cellular machinery through biological network comparisonQ36443509
Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping.Q36629048
Using a seed-network to query multiple large-scale gene expression datasets from the developing retina in order to identify and prioritize experimental targets.Q37328597
Altered expression of genes of the Bmp/Smad and Wnt/calcium signaling pathways in the cone-only Nrl-/- mouse retina, revealed by gene profiling using custom cDNA microarraysQ38338161
The Stanford Microarray DatabaseQ38661591
Gene expression profiles of mouse retinas during the second and third postnatal weeksQ40315875
Genetic rescue of cell number in a mouse model of microphthalmia: interactions between Chx10 and G1-phase cell cycle regulatorsQ44254916
BETA2/NeuroD1 null mice: a new model for transcription factor-dependent photoreceptor degeneration.Q44281884
Delayed expression of the Crx gene and photoreceptor development in the Chx10-deficient retinaQ44743277
Global gene expression analysis of the developing postnatal mouse retinaQ44777414
Rb regulates proliferation and rod photoreceptor development in the mouse retinaQ44780709
Efficient algorithms for detecting signaling pathways in protein interaction networksQ46097690
Systems biology 101--what you need to knowQ46351352
GenePath: a system for inference of genetic networks and proposal of genetic experiments.Q47643703
Functional and topological characterization of protein interaction networksQ47866212
Genetic Network Analyzer: qualitative simulation of genetic regulatory networks.Q48605631
BioMiner--modeling, analyzing, and visualizing biochemical pathways and networks.Q48617596
Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks.Q48647911
Fast and accurate alignment of multiple protein networks.Q51809838
The role of NeuroD as a differentiation factor in the mammalian retina.Q52178373
Identification of genetic networks from a small number of gene expression patterns under the Boolean network model.Q52211190
P4510describes a project that usesSQLQ47607
P304page(s)235-246
P577publication date2012-11-08
P1433published inBioinformatics and Biology InsightsQ4914913
P1476titleBioNetwork Bench: Database and Software for Storage, Query, and Analysis of Gene and Protein Networks
P478volume6

Search more.