• Representative journal articles about the field
• New journals devoted to systems biology
• Websites established by other organizations that are pursuing systems biology as their main focus of research

Several papers about systems biology have been written by ISB scientists and investigators at other institutions. A list of titles for representative publications is included below. To examine the abstracts in PubMed, open the following link and type the number provided for the PubMed ID (PMID) into the search window.

Representative articles authored by ISB scientists:

Aderem, A. “Systems biology: its practice and challenges.” Cell. 2005 May 20;121(4):511-3. PMID: 15907465

Aderem A, Smith KD. A systems approach to dissecting immunity and inflammation. Semin Immunol. 2004 Feb;16(1):55-67. PMID 14751764

Aebersold, R. “Molecular systems biology: a new journal for a new biology?” Molecular Systems Biology. 2005. doi:10.1038/msb4100009.

(No PMID citation)

Aitchison JD, Galitski T. Inventories to insights. J Cell Biol. 2003 May 12;161(3):465-9. PMID 12743099

Auffray C, Imbeaud S, Roux-Rouquie M, Hood L. From functional genomics to systems biology: concepts and practices. C R Biol. 2003 Oct-Nov;326(10-11):879-92. PMID 14744094

Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. Genome Res. 2004 Jun;14(6):1025-35. Epub 2004 May 12. PMID 15140832

Facciotti, MT, Boneau, R., Hood, L., Baliga, NS. Systems Biology Experimental Design--Considerations for building predictive gene regulatory network models for prokaryotic systems. 2004. Current Genomics 5:527-544. (No PMID citation)

Galitski, T. Molecular networks in model systems. Annu Rev Genomics Hum Genet. 2004;5:177-87. PMID: 15485347

Heath JR, Phelps ME, Hood L. NanoSystems biology. Mol Imaging Biol. 2003 Sep-Oct;5(5):312-25. PMID 14630511

Hood L, Heath JR, Phelps ME, Lin B. Systems biology and new technologies enable predictive and preventative medicine. Science. 2004 Oct 22;306(5696):640-3. PMID 15499008

Hood L. Systems biology: integrating technology, biology, and computation. Mech Ageing Dev. 2003 Jan;124(1):9-16. PMID 12618001

Ideker T, Galitski T, Hood L. A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet. 2001;2:343-72. PMID 11701654

SBML Forum (including Bolouri, H). The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003 Mar 1;19(4):524-31. PMID 12611808

Weston AD, Hood L. Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine. J Proteome Res. 2004 Mar-Apr;3(2):179-96. PMID 15113093

A large number of papers are now being published regarding the field of systems biology. A sample of articles authored by non-ISB investigators that covers a variety of perspectives on systems biology is presented.

Aggarwal K, Lee KH. Functional genomics and proteomics as a foundation for systems biology. Brief Funct Genomic Proteomic. 2003 Oct;2(3):175-84. PMID 15239921

Aloy P, Russell RB. Structure-based systems biology: a zoom lens for the cell. FEBS Lett. 2005 Mar 21;579(8):1854-8. PMID 15763563

Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet. 2004 Feb;5(2):101-13. PMID 14735121

Bialek W, Botstein D. Introductory science and mathematics education for 21st-Century biologists. Science. 2004 Feb 6;303(5659):788-90. PMID 14764865

de Jong H. Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol. 2002;9(1):67-103. PMID 11911796

Ehrenberg M, Elf J, Aurell E, Sandberg R, Tegner J. Systems biology is taking off. Genome Res. 2003 Nov;13(11):2377-80. PMID 14597651

Friboulet A, Thomas D. Systems Biology-an interdisciplinary approach. Biosens Bioelectron. 2005 Jun 15;20(12):2404-7. PMID 15854815

Huang S. Back to the biology in systems biology: what can we learn from biomolecular networks? Brief Funct Genomic Proteomic. 2004 Feb;2(4):279-97. PMID 15163364

Ideker T, Lauffenburger D. Building with a scaffold: emerging strategies for high- to low-level cellular modeling. Trends Biotechnol. 2003 Jun;21(6):255-62. PMID 12788545

Ideker T. Systems biology 101--what you need to know. Nat Biotechnol. 2004 Apr;22(4):473-5. PMID 15085805

Kell DB. Metabolomics and systems biology: making sense of the soup. Curr Opin Microbiol. 2004 Jun;7(3):296-307. PMID 15196499

Kell DB, Oliver SG. Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era. Bioessays. 2004 Jan;26(1):99-105. PMID 14696046

Kitano H. Systems biology: a brief overview. Science. 2002 Mar 1;295(5560):1662-4. PMID 11872829

Kitano H. Looking beyond the details: a rise in system-oriented approaches in genetics and molecular biology. Curr Genet. 2002 Apr;41(1):1-10. Epub 2002 Apr 4. PMID 12073094

Levchenko A Dynamical and integrative cell signaling: challenges for the new biology. Biotechnol Bioeng. 2003 Dec 30;84(7):773-82. PMID 14708118

Levesque MP, Benfey PN. Systems biology. Curr Biol. 2004 Mar 9;14(5):R179-80. PMID 15028228

Lindon JC, Holmes E, Nicholson JK. Metabonomics: systems biology in pharmaceutical research and development. Curr Opin Mol Ther. 2004 Jun;6(3):265-72. PMID 15264428

Mahadevan R, Palsson BO. Properties of metabolic networks: structure versus function. Biophys J. 2005 Jan;88(1):L07-9. Epub 2004 Dec 1. PMID 15574705

Moore JH, Williams SM. Traversing the conceptual divide between biological and statistical epistasis: systems biology and a more modern synthesis. Bioessays. 2005 Jun;27(6):637-46. PMID 15892116

Morel NM, Holland JM, van der Greef J, Marple EW, Clish C, Loscalzo J, Naylor S. Primer on medical genomics. Part XIV: Introduction to systems biology--a new approach to understanding disease and treatment. Mayo Clin Proc. 2004 May;79(5):651-8. PMID 15132407

Noble D. The future: putting Humpty-Dumpty together again. Biochem Soc Trans. 2003 Feb;31(Pt 1):156-8. PMID 12546675

Uetz P, Finley RL Jr. From protein networks to biological systems. FEBS Lett. 2005 Mar 21;579(8):1821-7. PMID 15763558

Vidal M. Interactome modeling. FEBS Lett. 2005 Mar 21;579(8):1834-8. PMID 15763560

Westerhoff HV, Palsson BO. The evolution of molecular biology into systems biology. Nat Biotechnol. 2004 Oct;22(10):1249-52. PMID 15470464

Wolkenhauer O. Systems biology: the reincarnation of systems theory applied in biology?Brief Bioinform. 2001 Sep;2(3):258-70. PMID 11589586

Wyrick JJ, Young RA. Deciphering gene expression regulatory networks. Curr Opin Genet Dev. 2002 Apr;12(2):130-6. PMID 11893484

Zaslaver A, Mayo AE, Rosenberg R, Bashkin P, Sberro H, Tsalyuk M, Surette MG, Alon U. Just-in-time transcription program in metabolic pathways. Nat Genet. 2004 May;36(5):486-91. Epub 2004 Apr 25. PMID 15107854

Systems Biology-oriented journals:

One sign that a discipline has “arrived” is the creation of peer-review professional journals explicitly devoted to the discipline’s subject matter. The following three newly created journals are likely to be the first of many more to come.

Molecular Systems Biology

http://www.nature.com/msb/index.html

Systems Biology

http://www.iee.org/Publish/Journals/ProfJourn/Sb/index.cfm

OMICS: A journal of integrative biology

http://www.liebertpub.com/publication.aspx?pub_id=43

In light of the need to establish cross-disciplinary teams of investigators for systems biology research, a number of systems biology centers or coalitions have been created during the past five years, beginning with us at the Institute for Systems Biology in Seattle. A partial list is presented here.

Systems Biology organizations and web sites:

Institute for Systems Biology

http://www.systemsbiology.org

Department of Systems Biology, Harvard Medical School

http://sysbio.med.harvard.edu/

Molecular Sciences Institute (Berkeley)

http://www.molsci.org/Dispatch

Computational and Systems Biology Initiative (MIT)

http://csbi.mit.edu

Lewis Siegler Institute for Integrative Genomics (Princeton)

http://www.genomics.princeton.edu/

Center for Systems Biology, Institute for Advanced Study (Princeton)

http://www.csb.ias.edu/

Systems Biology at PNNL (Pacific Northwest National Laboratory)

http://www.sysbio.org/

Keck Computational Systems Biology (California)

http://sbw.kgi.edu/

The Systems Biology Institute (Japan)

http://www.sbi.jp/indexE.html

Ottowa Institute of Systems Biology (Canada)

http://mededu.med.uottawa.ca/oisb/eng/

Systems Biology Group at the University of Stuttgart (Germany)

http://www.sysbio.de/