RegulonDB

swMATH25948MaRDI QIDQ37681FDOQ37681

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Official website: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238961/

Cited In (88)

• Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea
• Characteristics of promoter architecture-dependent expression noise and bursting kinetics
• Modeling for evolving biological networks with scale-free connectivity, hierarchical modularity, and disassortativity
• Operon prediction based on SVM
• A modified Ising model of Barabási-Albert network with gene-type spins
• Gene regulatory networks. Methods and protocols
• Fast computing global structural balance in signed networks based on memetic algorithm
• Binding of transcription factors adapts to resolve information-energy tradeoff
• Genome size and operon content
• A hybrid promoter analysis methodology for prokaryotic genomes
• Computational challenges in systems biology
• Wilks' \(\Lambda \) dissimilarity measures for gene clustering: an approach based on the identification of transcription modules
• Bayesian joint modeling of multiple gene networks and diverse genomic data to identify target genes of a transcription factor
• Directionality of real world networks as predicted by path length in directed and undirected graphs
• Dynamics of transcription of closely spaced promoters in \textit{Escherichia coli}, one event at a time
• Transcription factor binding sites detection by using alignment-based approach
• SOLNP
• TRESNEI
• SIMoNe
• E-CELL
• EDISON
• G1DBN
• MetaCyc
• gNCA
• Footprinter
• BioProspector
• GGMselect
• HPAM
• SynTReN
• LTR_FINDER
• Netsim
• BiNGO
• CLENCH
• ARACNE
• PlantTFDB
• SIRENE
• bc3net
• WebLogo
• JASPAR
• Matrix eQTL
• GeneNetWeaver
• GeneMarkS
• NARROMI
• BacPP
• ANAT
• BGRMI
• BioPreDyn-bench
• CopraRNA
• Diurnal
• DREM
• DINGO
• GeneSPIDER
• GeNGe
• IntaRNA
• IntScore
• LASSIE
• MMG
• NetBenchmark
• Netter
• Path2Models
• REDfly
• SGN Sim
• sgnesR
• SPINE
• SOSlib
• TRaCE+
• PSoL
• CplexA
• Dizzy
• PhyME
• GNA
• DREAM4
• REVEAL
• JDINAC
• A mixed-integer optimization framework for the synthesis and analysis of regulatory networks
• Modeling and analysis of gene regulatory networks
• Ranking of network elements based on functional substructures
• Embedding of biological regulatory networks and property preservation
• The recognition and prediction of \(\sigma^{70}\) promoters in \textit{Escherichia coli} K-12
• Computational prediction of conserved operons and phylogenetic footprinting of transcription regulatory elements in the metal-reducing bacterial family \textit{Geobacteraceae}
• Modeling promoter search by \textit{E. coli} RNA polymerase: one-dimensional diffusion in a sequence-dependent energy landscape
• Mathematical conditions for induced cell differentiation and trans-differentiation in adult cells
• Bayesian Variational Inference for Exponential Random Graph Models
• Effects of alternative connectivity on behavior of randomly constructed Boolean networks
• BacPP: bacterial promoter prediction -- a tool for accurate sigma-factor specific assignment in enterobacteria
• Constrained community-based gene regulatory network inference
• Information content based model for the topological properties of the gene regulatory network of \textit{Escherichia coli}
• Regulatory dynamics of standard two-component systems in bacteria

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