Functional genomics, proteomics, metabolomics and bioinformatics for systems biology

Stéphane Ballereau; Enrico Glaab; Alexei Kolodkin; Amphun Chaiboonchoe; Maria Biryukov; Nikos Vlassis; Hassan Ahmed; Johann Pellet; Nitin Baliga; Leroy Hood; Reinhard Schneider; Rudi Balling; Charles Auffray

doi:10.1007/978-94-007-6803-1_1

Functional genomics, proteomics, metabolomics and bioinformatics for systems biology

Stéphane Ballereau^*, Enrico Glaab, Alexei Kolodkin, Amphun Chaiboonchoe, Maria Biryukov, Nikos Vlassis, Hassan Ahmed, Johann Pellet, Nitin Baliga, Leroy Hood, Reinhard Schneider, Rudi Balling, Charles Auffray

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

6 Citations (Scopus)

Abstract

This chapter introduces Systems Biology, its context, aims, concepts and strategies, then describes approaches used in genomics, epigenomics, transcriptomics, proteomics, metabolomics and lipidomics, and how recent technological advances in these fields have moved the bottleneck from data production to data analysis. Methods for clustering, feature selection, prediction analysis, text mining and pathway analysis used to analyse and integrate the data produced are then presented.

Original language	English
Title of host publication	Systems Biology
Subtitle of host publication	Integrative Biology and Simulation Tools
Publisher	Springer Netherlands
Pages	3-41
Number of pages	39
Volume	1
ISBN (Electronic)	9789400768031
ISBN (Print)	9789400768024
DOIs	https://doi.org/10.1007/978-94-007-6803-1_1
Publication status	Published - 1 Jan 2013
Externally published	Yes

Keywords

Bioinformatics
Bottom-up
Clustering
Curse of dimensionality
Data integration
Emergence
Epigenomics
Feature selection
Functional genomics
High-dimensionality
High-throughput
Holistic
Interactions
Knowledge management
Mass spectrometry
Mathematical model
Metabolomics
Middle-out
Network
Next generation sequencing
Ontology
Pathway
Prediction analysis
Proteomics
Text-mining
Top-down
Transcriptomics

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10.1007/978-94-007-6803-1_1

Cite this

Ballereau, S., Glaab, E., Kolodkin, A., Chaiboonchoe, A., Biryukov, M., Vlassis, N., Ahmed, H., Pellet, J., Baliga, N., Hood, L., Schneider, R., Balling, R., & Auffray, C. (2013). Functional genomics, proteomics, metabolomics and bioinformatics for systems biology. In Systems Biology: Integrative Biology and Simulation Tools (Vol. 1, pp. 3-41). Springer Netherlands. https://doi.org/10.1007/978-94-007-6803-1_1

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abstract = "This chapter introduces Systems Biology, its context, aims, concepts and strategies, then describes approaches used in genomics, epigenomics, transcriptomics, proteomics, metabolomics and lipidomics, and how recent technological advances in these fields have moved the bottleneck from data production to data analysis. Methods for clustering, feature selection, prediction analysis, text mining and pathway analysis used to analyse and integrate the data produced are then presented.",

keywords = "Bioinformatics, Bottom-up, Clustering, Curse of dimensionality, Data integration, Emergence, Epigenomics, Feature selection, Functional genomics, High-dimensionality, High-throughput, Holistic, Interactions, Knowledge management, Mass spectrometry, Mathematical model, Metabolomics, Middle-out, Network, Next generation sequencing, Ontology, Pathway, Prediction analysis, Proteomics, Text-mining, Top-down, Transcriptomics",

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Ballereau, S, Glaab, E, Kolodkin, A, Chaiboonchoe, A, Biryukov, M, Vlassis, N, Ahmed, H, Pellet, J, Baliga, N, Hood, L, Schneider, R, Balling, R & Auffray, C 2013, Functional genomics, proteomics, metabolomics and bioinformatics for systems biology. in Systems Biology: Integrative Biology and Simulation Tools. vol. 1, Springer Netherlands, pp. 3-41. https://doi.org/10.1007/978-94-007-6803-1_1

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T1 - Functional genomics, proteomics, metabolomics and bioinformatics for systems biology

AU - Ballereau, Stéphane

AU - Glaab, Enrico

AU - Kolodkin, Alexei

AU - Chaiboonchoe, Amphun

AU - Biryukov, Maria

AU - Vlassis, Nikos

AU - Ahmed, Hassan

AU - Pellet, Johann

AU - Baliga, Nitin

AU - Hood, Leroy

AU - Schneider, Reinhard

AU - Balling, Rudi

AU - Auffray, Charles

N1 - Publisher Copyright: © Springer Science+Business Media Dordrecht 2013.

PY - 2013/1/1

Y1 - 2013/1/1

N2 - This chapter introduces Systems Biology, its context, aims, concepts and strategies, then describes approaches used in genomics, epigenomics, transcriptomics, proteomics, metabolomics and lipidomics, and how recent technological advances in these fields have moved the bottleneck from data production to data analysis. Methods for clustering, feature selection, prediction analysis, text mining and pathway analysis used to analyse and integrate the data produced are then presented.

AB - This chapter introduces Systems Biology, its context, aims, concepts and strategies, then describes approaches used in genomics, epigenomics, transcriptomics, proteomics, metabolomics and lipidomics, and how recent technological advances in these fields have moved the bottleneck from data production to data analysis. Methods for clustering, feature selection, prediction analysis, text mining and pathway analysis used to analyse and integrate the data produced are then presented.

KW - Bioinformatics

KW - Bottom-up

KW - Clustering

KW - Curse of dimensionality

KW - Data integration

KW - Emergence

KW - Epigenomics

KW - Feature selection

KW - Functional genomics

KW - High-dimensionality

KW - High-throughput

KW - Holistic

KW - Interactions

KW - Knowledge management

KW - Mass spectrometry

KW - Mathematical model

KW - Metabolomics

KW - Middle-out

KW - Network

KW - Next generation sequencing

KW - Ontology

KW - Pathway

KW - Prediction analysis

KW - Proteomics

KW - Text-mining

KW - Top-down

KW - Transcriptomics

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U2 - 10.1007/978-94-007-6803-1_1

DO - 10.1007/978-94-007-6803-1_1

M3 - Chapter

AN - SCOPUS:84948115067

SN - 9789400768024

VL - 1

SP - 3

EP - 41

BT - Systems Biology

PB - Springer Netherlands

ER -

Functional genomics, proteomics, metabolomics and bioinformatics for systems biology

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