ISU Systems Biology Club

Some Papers on Systems Biology

Systems Biology: Toward System-level Understanding of Biological Systems
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
Poster: The Systems Biology Workbench (SBW) Version 1.0: Framwork and Modules
New Computational Approaches for Analysis of cis-Regulatory Networks.
Computational tools for reconstructing genetic regulatory networks
Modeling DNA sequence-Based cis-Regulatory Gene Networks
Cis-regulatory logic in the endo16 gene: switching from a specification to a differentiation mode of control
Genomic Cis-Regulatory Logic: Experimental and Computational Analysis of a Sea Urchin Gene
Modeling transcriptional regulatory networks
Logical Modeling of Developmental Genetic Regulatory Networks with NetBuilder
Robustness as a Measure of Plausibility in Models of Biochemical Networks
Nikolau BJ, Fien O, Wurtele ES 2005 (anticipated January) Plant Metabolomics. Kluwer Academic Publishers
Dickerson JA, Yang Y, Blom K, Reinot A, Lie J, Cruz-Neira C, Wurtele ES. 2003. Using Virtual Reality to Understand Complex Metabolic Networks. Atlantic Symposium. In press
Wurtele ES, Li J, Diao L, Zhang H, Foster CM, Fatland B, Julie Dickerson J, Brown A, Cox Z, Cook D, Lee E-K, Hofmann H. 2003. MetNet: Software to build and model the biogenetic lattice of Arabidopsis. Comp Funct Genom 4: 239-245.
Dickerson JA, Yang Y, Blom K, Reinot A, Lie J, Cruz-Neira C, Wurtele ES. 2003. "Using Virtual Reality to Understand Complex Metabolic Networks." Atlantic Symposium on Computational Biology and Genomic Information Systems and Technology, September. In press.
Oliver DJ, Nikolau BJ. Wurtele ES. 2002 Functional Genomics: High throughput mRNA, protein, and metabolite analyses, Metabolic engineering. 4:98-108.
Dickerson JA, Berleant, D, Cox Z, Qi, W, Ashlock D, Fulmer AW, Wurtele ES, 2003 “Creating and Modeling Metabolic and Regulatory Networks Using Text Mining and Expert Knowledge,” in Computational Biology and Genome Informatics, edited by Cathy H. Wu, Paul Wang, Jason T. L. Wang, World Scientific. Chapter 9. pp. 1-33.
Ding J, Berleant D, Nettleton D, E. Wurtele ES. 2002. Mining Medline: Abstracts, sentences, or phrases? Pacific Symposium on Biocomputing, 1-12. Pacific Symposium on Biocomputing (PSB 2002), Kaua'i, Hawaii, Jan. 3-7, pp. 326-337.
Dickerson JA, Cox Z, Wurtele ES,, Fulmer AW, 2001“Creating metabolic and regulatory network models using fuzzy cognitive maps,” IFSA World Congress and 20th North American Fuzzy Information Processing Society (NAFIPS) International Conference, Vancouver, British Columbia, Volume 4, 2171-2176, July, 2001
Wuchty etal BioNetworks_Sept03 preprnt
Albert,Barabasi RevModPhys 2002 74, 47-97
Almaas etal Nature2004 427,839-843
Barabasi etal Physica 1999 A272,173-187
Barabasi,Bonabeau Scient Amer May03 50-59
Barabasi,Oltvai NatureRevGenet 2004 5,101-114
deMenezes,Barabasi PhysRevLett 2004 92,028701_1-4
Dobrin etal BMC Bioinformatics 2004 5_10
Goh etal arXivcond-mat_0205232_v2_10Oct2002
Jeong etal Nature 2001 411,41-42
Williams etal PNAS 2002 99,12913-12916
Schwikowski Nat Biotech 2000 18,1257-1261
Atilgan etal BiophysJ 2004 86,85-91

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