Gene regulatory networks. Methods and protocols

DOI10.1007/978-1-4939-8882-2zbMATH Open1417.92005OpenAlexW2913354234MaRDI QIDQ1721981FDOQ1721981

Author name not available (Why is that?)

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)

Cites Work

• NOMAD

Cited In (9)

• Learning the structure of the mTOR protein signaling pathway from protein phosphorylation data
• Percolation on the gene regulatory network
• Challenges for machine learning in RNA-protein interaction prediction
• 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
• Improved baselines for causal structure learning on interventional data
• Regulatory Signals in Genomic Sequences
• 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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