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

noisedifferential expressionRNA-seqbig dataregulatory networksmicroRNAprotein-protein interaction networkhost-parasite interactiongenome wide association studyATAC-seqcell cycle transitioncomputational prediction of protein complexcontext filteringdrug toxicity predictiondynamic signallingepigenetic landscapefluorescence activated cell sortinglong non-coding RNAmiRNA-target interaction networkmulti-omicsmultilayer regulatory networksqualitative modelling of regulatory networksrule-based methodsspatial analysis of functional enrichment (SAFE)virus-host interaction

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) Cell biology (92C37)

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Cited in

(5)

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

Describes a project that uses

Uses Software

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

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