Hlavacek:Publications: Difference between revisions

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==Recent work==
==Recent work==


*Mu F, Unkefer CJ, Unkefer PJ, Hlavacek WS (2011) Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds. [http://bioinformatics.oxfordjournals.org/ Bioinformatics]  
*Chylek LA, Wilson BS, Hlavacek WS (2012) Modeling biomolecular site dynamics in immunoreceptor signaling systems. Los Alamos Technical Report LA-UR-12-23058 [[media:LA-UR-12-23058.pdf|pdf]]


*Lemons NW, Hu B, Hlavacek WS (2011) Hierarchical graphs for rule-based modeling of biochemical systems. [http://www.biomedcentral.com/bmcbioinformatics BMC Bioinformatics] '''12''':45 PMID 21288338
*Chylek LA, Stites EC, Posner RG, Hlavacek WS (2012) Innovations of the rule-based modeling approach. Los Alamos Technical Report LA-UR-12-10375 [[media:LA-UR-12-10375.pdf|pdf]]


*Bauer AL, Hlavacek WS, Unkefer PJ, Mu F (2010) Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites. [http://www.ploscompbiol.org PLoS Comput Biol] '''6''':e1001007 PMID 21124945
*Creamer MS, Stites EC, Aziz M, Cahill JA, Tan CW, Berens ME, Von Hoff DD, Hlavacek WS, Posner RG (2012) Visualization, annotation and simulation of a large rule-based model for ErbB receptor signaling. BMC Syst Biol 6:107 PMID 22913808
 
*Barua D, Hlavacek WS, Lipniacki T (2012) A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn. J Immunol 189:646-658. PMID 22711887


==Selected publications==
==Selected publications==


*Wall ME, Hlavacek WS, Savageau MA (2004) Design of gene circuits: lessons from bacteria. [http://www.nature.com/nrg/index.html Nat Rev Genet] '''5''', 34-42 PMID 14708014
*Hlavacek WS, Faeder JR, Blinov ML, Perelson AS, Goldstein B (2003) The complexity of complexes in signal transduction. [http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1097-0290 Biotechnol Bioeng] '''84''', 783-794. PMID 14708119
 
*Wall ME, Hlavacek WS, Savageau MA (2004) Design of gene circuits: lessons from bacteria. [http://www.nature.com/nrg/index.html Nat Rev Genet] '''5''', 34-42. PMID 14708014
 
*Goldstein B, Faeder JR, Hlavacek WS (2004) Mathematical and computational models of immune-receptor signalling. [http://www.nature.com/nri/index.html Nat Rev Immunol] '''4''', 445-456. PMID 15173833
 
*Blinov ML, Faeder JR, Goldstein B, Hlavacek WS (2004) BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. [http://bioinformatics.oxfordjournals.org/ Bioinformatics] '''20''', 3289-3291. PMID 15217809


*Hlavacek WS, Faeder JR, Blinov ML, Posner RG, Hucka M, Fontana W (2006) Rules for modeling signal-transduction systems. [http://stke.sciencemag.org/ Sci STKE] '''2006''', re6. PMID 16849649
*Hlavacek WS, Faeder JR, Blinov ML, Posner RG, Hucka M, Fontana W (2006) Rules for modeling signal-transduction systems. [http://stke.sciencemag.org/ Sci STKE] '''2006''', re6. PMID 16849649

Revision as of 19:43, 6 December 2012

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Recent work

  • Chylek LA, Wilson BS, Hlavacek WS (2012) Modeling biomolecular site dynamics in immunoreceptor signaling systems. Los Alamos Technical Report LA-UR-12-23058 pdf
  • Chylek LA, Stites EC, Posner RG, Hlavacek WS (2012) Innovations of the rule-based modeling approach. Los Alamos Technical Report LA-UR-12-10375 pdf
  • Creamer MS, Stites EC, Aziz M, Cahill JA, Tan CW, Berens ME, Von Hoff DD, Hlavacek WS, Posner RG (2012) Visualization, annotation and simulation of a large rule-based model for ErbB receptor signaling. BMC Syst Biol 6:107 PMID 22913808
  • Barua D, Hlavacek WS, Lipniacki T (2012) A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn. J Immunol 189:646-658. PMID 22711887

Selected publications

  • Hlavacek WS, Faeder JR, Blinov ML, Perelson AS, Goldstein B (2003) The complexity of complexes in signal transduction. Biotechnol Bioeng 84, 783-794. PMID 14708119
  • Wall ME, Hlavacek WS, Savageau MA (2004) Design of gene circuits: lessons from bacteria. Nat Rev Genet 5, 34-42. PMID 14708014
  • Goldstein B, Faeder JR, Hlavacek WS (2004) Mathematical and computational models of immune-receptor signalling. Nat Rev Immunol 4, 445-456. PMID 15173833
  • Blinov ML, Faeder JR, Goldstein B, Hlavacek WS (2004) BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. Bioinformatics 20, 3289-3291. PMID 15217809
  • Hlavacek WS, Faeder JR, Blinov ML, Posner RG, Hucka M, Fontana W (2006) Rules for modeling signal-transduction systems. Sci STKE 2006, re6. PMID 16849649
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