Gene regulatory networks. Methods and protocols

DOI10.1007/978-1-4939-8882-2MaRDI QIDQ1721981zbMATH OpenOpenAlexFDO

Authors

Publication date 13 February 2019

Published in Methods in Molecular Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/978-1-4939-8882-2

zbMATH Keywords

Bayesian networkdecision treeensemble methodsintegrative analysisobservational datarandom forestordinary differential equationsgene regulatory networkdifferential module networksgenome scalesingle-cell datasmall networkstability inferencestatistical network inferencetimeseries

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Systems biology, networks (92C42) Proceedings, conferences, collections, etc. pertaining to biology (92-06) Computational methods for problems pertaining to biology (92-08)

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Cites work

• NOMAD

Cited in

(19)

• Inferring dynamic gene regulatory networks with low-order conditional independencies -- an evaluation of the method
• Automated inference of gene regulatory networks using explicit regulatory modules
• Influence of statistical estimators on the large-scale causal inference of regulatory networks
• Learning the structure of the mTOR protein signaling pathway from protein phosphorylation data
• Percolation on the gene regulatory network
• Autoregressive models for gene regulatory network inference: sparsity, stability and causality issues
• Network inference and biological dynamics
• Introduction to biological networks
• Challenges for machine learning in RNA-protein interaction prediction
• Evolutionary computation in gene regulatory network research
• scientific article; zbMATH DE number 6724264 (Why is no real title available?)
• A novel robust estimation for high-dimensional precision matrices
• Genetic networks: processing data, regulatory network modelling and their analysis
• CSI: a nonparametric Bayesian approach to network inference from multiple perturbed time series gene expression data
• WENDY: covariance dynamics based gene regulatory network inference
• Improved baselines for causal structure learning on interventional data
• Regulatory Signals in Genomic Sequences
• A survey of models for inference of gene regulatory networks
• Interpretable polynomial neural ordinary differential equations

Describes a project that uses

Uses Software

• Path2Models
• SOSlib
• LASSIE
• BioPreDyn-bench
• MMG
• sgnesR
• GeNGe
• SGN Sim
• IntaRNA
• CopraRNA
• IntScore
• SINCERITIES
• BGRMI
• TRaCE+
• GeneSPIDER
• DINGO
• Netter
• REDfly
• SCODE
• SCENIC
• dynGENIE3
• NetBenchmark
• ANAT
• SPINE
• DREM
• Diurnal
• bnstruct
• systemPipeR
• PESTO
• RegulonDB
• Data2Dynamics
• NARROMI
• TIGRESS
• GeneNetWeaver
• UniProt
• ORBIT
• Matrix eQTL
• JASPAR
• sva
• DGCA
• BioGRID
• SIRENE
• FIMO
• ARACNE
• PlantTFDB
• BiNGO
• KEGG
• SynTReN
• COPASI
• QUIC
• FATODE
• MultiNest
• GGMselect
• MEIGO
• huge
• EDISON
• bnlearn
• BioBayes
• E-CELL
• fdrtool
• glasso
• WGCNA
• KLU
• SIMoNe
• NL2SOL
• TRESNEI
• SOLNP
• CVODES
• BOBYQA
• COMSOL
• NOMAD
• Bio-PEPA
• SUNDIALS
• STRSCNE
• PSwarm
• R

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