Home

Labs

Systems Biology Resources

The following is a list of useful links to various online resources for systems biologists and people with a general interest in systems biology. If you would like to share a useful link, please send us the URL through Contact Us.

Systems Biology Institutes and Departments


Center for Algorithmic and Systems Biology - http://casb.ucsd.edu/
Institute for Systems Biology - http://www.systemsbiology.org/
Department of Systems Biology at Harvard Medical School - http://sysbio.med.harvard.edu/
Systems Biology at Pacific Northwest National Laboratory - http://www.sysbio.org/
The International Society for Systems Biology - http://issb.org/
The Systems Biology Institute - http://sbi.jp/
Centre for Integrative Systems Biology at Imperial College - http://www3.imperial.ac.uk/cisbic
The Molecular Sciences Institute - http://www.molsci.org/index.html

Journals most relevant to Systems Biology


Molecular Systems Biology - http://www.nature.com/msb/index.html
BMC Systems Biology - http://www.biomedcentral.com/bmcsystbiol/
Genome Biology - http://genomebiology.com/home/
Bioinformatics - http://bioinformatics.oxfordjournals.org/
BMC Bioinformatics - http://www.biomedcentral.com/bmcbioinformatics/
Journal of Theoretical Biology - http://www.elsevier.com/wps/find/journaldescription.cws_home/622904/description£description
PLoS Computational Biology - http://www.ploscompbiol.org/home.action
Biosystems - http://www.elsevier.com/wps/find/journaldescription.cws_home/506017/description£description

Online Tools for Systems Biology


PathBlast - http://www.pathblast.org/
KEGG: Kyoto Encyclopedia of Genes and Genomes - http://www.genome.jp/kegg/
Systems Biology Workbench - http://sbw.sourceforge.net/
The Systems Biology Markup Language - http://sbml.org/Main_Page
CellDesigner - http://systems-biology.org/software/celldesigner/
Cytoscape - http://www.cytoscape.org
CellNetAnalyzer/FluxAnalyzer - http://www.mpi-magdeburg.mpg.de/projects/cna/cna.html
NetBuilder - http://strc.herts.ac.uk/bio/maria/NetBuilder/
BioTapestry - http://www.biotapestry.org/
Virtual Cell - http://www.vcell.org/
E-cell - http://www.e-cell.org/ecell/

Literature on Systems Biology

	Books
An Introduction to Systems Biology: Design Principles of Biological Circuits - Uri Alon (2006) Chapman & Hall/CRC
Systems Biology: Properties of Reconstructed Networks - Bernhard O. Palsson (2006) Cambridge University Press
Foundations of Systems Biology - Edited by Hiroaki Kitano (2001) The MIT Press
Introduction to Systems Biology - Edited by Sangdun Choi (2007) Humana Press/Springer
The Regulatory Genome: Gene Regulatory Networks In Development And Evolution - Eric H. Davidson (2006) Academic Press
Linked: How Everything Is Connected to Everything Else and What It Means - Albert-Laszlo Barabassi (2003) Plume

	Review Articles
Kitano H. Biological robustness. Nat Rev Genet. 2004 Nov;5(11):826-37. Review. PMID: 15520792 [PubMed - indexed for MEDLINE]
Kitano H. Systems biology: a brief overview. Science. 2002 Mar 1;295(5560):1662-4. Review. PMID: 11872829 [PubMed - indexed for MEDLINE]
Csete ME, Doyle JC. Reverse engineering of biological complexity. Science. 2002 Mar 1;295(5560):1664-9. Review.
Stelling J, Sauer U, Szallasi Z, Doyle FJ 3rd, Doyle J. Robustness of cellular functions. Cell. 2004 Sep 17;118(6):675-85. Review.
Barabási AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet. 2004 Feb;5(2):101-13. Review.
Ideker T, Galitski T, Hood L. A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet. 2001;2:343-72. Review.
Ge H, Walhout AJ, Vidal M. Integrating 'omic' information: a bridge between genomics and systems biology. Trends Genet. 2003 Oct;19(10):551-60. Review.
Alon U. Network motifs: theory and experimental approaches. Nat Rev Genet. 2007 Jun;8(6):450-61. Review.
Albert R. Scale-free networks in cell biology. J Cell Sci. 2005 Nov 1;118(Pt 21):4947-57. Review.

Other interesting sites


Systems Biology @ Nature - http://www.nature.com/sysbio/index.html
BMC Systems Biology Gateway - http://www.biomedcentral.com/gateways/systemsbiology
The Systems Biology Institute portal - http://systems-biology.org/


UCSD	GNF	BURNHAM	SALK	TSRI

sponsors:	454 Sequencing		Agilent		Ambry Genetics		Applied Biosystems
	Dharmacon		Illumnina		Open Biosystems		QIAGEN