Computational cell biology. Methods and protocols

DOI10.1007/978-1-4939-8618-7MaRDI QIDQ1721982zbMATH 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/10.1007/978-1-4939-8618-7

zbMATH Keywords

long non-coding RNAvirus-host interactionspatial analysis of functional enrichment (SAFE)rule-based methodsRNA-seqregulatory networksqualitative modelling of regulatory networksprotein-protein interaction networknoisemultilayer regulatory networksmulti-omicsmiRNA-target interaction networkmicroRNAATAC-seqhost-parasite interactiongenome wide association studyfluorescence activated cell sortingepigenetic landscapedynamic signallingdrug toxicity predictiondifferential expressioncontext filteringcomputational prediction of protein complexcell cycle transitionbig data

Mathematics Subject Classification ID

Proceedings, conferences, collections, etc. pertaining to biology (92-06) Computational methods for problems pertaining to biology (92-08) Cell biology (92C37) Biochemistry, molecular biology (92C40) Systems biology, networks (92C42)

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Cited in

(5)

• Biocomputing system of living cells
• Cell Mapping Methods
• Elements of computational systems biology.
• scientific article; zbMATH DE number 2241899 (Why is no real title available?)
• Extrapolation is not the same as interpolation

Describes a project that uses

Uses Software

• Cytoscape
• Graphviz
• Bioconductor
• gplots
• PLINK
• gcrma
• edgeR
• igraph
• WGCNA
• GEOquery
• PISKaS
• COPASI
• Dynagraph
• BioNet
• KEGG
• RedeR
• Cellnoptr
• iPath
• TopHat
• BoolNet
• Kappa
• inSilicoDb
• BioGRID
• CellNOpt
• IntAct
• ClueGO
• ChemSpot
• GCTA
• STRING
• R
• WikiPathways
• PISKa
• KaSim
• HIPPIE
• DISEASES
• dmGWAS
• GWAPP
• SignaLink
• iHOP
• VirusMentha
• dbPTM
• HuPho
• InnateDB
• MatrixDB
• Negatome
• Phospho.ELM
• iPfam
• PIBASE
• NPInter
• ConsensusPathDB
• SQUAD
• Jimena
• miRNet
• miRecords
• SM2miR
• EpimiR
• HTqPCR
• miRTarBase
• YEASTRACT
• RTCGA
• inSilicoMerging
• ProtNet
• DOMINE
• IDDI
• MOPED
• PaxDb
• AlzPathway
• ATtRACT
• VirHostNet
• GNAT
• PathCellNet
• SMPDB
• NET-SYNTHESIS
• PRS
• ANIMO
• STRINGdb
• COMPARTMENTS

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