Gene regulatory networks. Methods and protocols
DOI10.1007/978-1-4939-8882-2zbMATH Open1417.92005OpenAlexW2913354234MaRDI QIDQ1721981FDOQ1721981
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
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Bayesian networkdecision treeensemble methodsintegrative analysisobservational datarandom forestordinary differential equationsgene regulatory networkdifferential module networksgenome scalesingle-cell datasmall networkstability inferencestatistical network inferencetimeseries
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)
Cites Work
Cited In (18)
- Automated inference of gene regulatory networks using explicit regulatory modules
- Inferring dynamic gene regulatory networks with low-order conditional independencies -- an evaluation of the method
- 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
- Title not available (Why is that?)
- 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
- 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
Uses Software
- R
- PSwarm
- STRSCNE
- SUNDIALS
- Bio-PEPA
- NOMAD
- COMSOL
- BOBYQA
- CVODES
- SOLNP
- TRESNEI
- NL2SOL
- SIMoNe
- KLU
- WGCNA
- glasso
- fdrtool
- E-CELL
- BioBayes
- bnlearn
- EDISON
- huge
- MEIGO
- GGMselect
- MultiNest
- FATODE
- QUIC
- COPASI
- SynTReN
- KEGG
- BiNGO
- PlantTFDB
- ARACNE
- FIMO
- SIRENE
- BioGRID
- DGCA
- sva
- JASPAR
- Matrix eQTL
- ORBIT
- UniProt
- GeneNetWeaver
- TIGRESS
- NARROMI
- Data2Dynamics
- RegulonDB
- PESTO
- systemPipeR
- bnstruct
- Diurnal
- DREM
- SPINE
- ANAT
- NetBenchmark
- dynGENIE3
- SCENIC
- SCODE
- REDfly
- Netter
- DINGO
- GeneSPIDER
- TRaCE+
- BGRMI
- SINCERITIES
- IntScore
- CopraRNA
- IntaRNA
- SGN Sim
- GeNGe
- sgnesR
- MMG
- BioPreDyn-bench
- LASSIE
- SOSlib
- Path2Models
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