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Andrew R. Joyce, PhD

Zedler BK, Joyce A, Murrelle L, Kakad P, Harpe SE. A pharmacoepidemiologic analysis of the impact of calendar packaging on adherence to self-administered medications for long-term use. Clin Ther. 33(5): 581-97, 2011. PMID: 21665043

Applebee MK, Joyce AR, Conrad TM, Pettigrew DW, Palsson BØ. Functional and metabolic effects of adaptive glycerol kinase (GLPK) mutants in Escherichia coli. J Biol Chem. 286(26):23150-9, 2011. PMID: 21550976

Conrad TM, Frazier M, Joyce AR, Cho BK, Knight EM, Lewis NE, Landick R, Palsson BØ. RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media. Proc Natl Acad Sci U S A. 107(47):20500-5, 2010. PMID: 21057108

Edmiston JS, Archer KJ, Scian MJ, Joyce AR, Zedler BK, Murrelle EL. Gene expression profiling of peripheral blood leukocytes identifies potential novel biomarkers of chronic obstructive pulmonary disease in current and former smokers. Biomarkers. 15(8):715-30, 2010. PMID: 20887155

Joyce AR, Hawkins W, Fariss MW, Sengupta TK. Role of plasma membrane disruption in reference moist smokeless tobacco-induced cell death. Toxicol Lett. 198(2):191-9, 2010. PMID: 20600711

Meng H, Joyce AR, Adkins DE, Basu P, Jia Y, Li G, Sengupta TK, Zedler BK, Murrelle EL, van den Oord EJCG: A statistical method for excluding non-variable CpG sites in high-throughput DNA methylation profiling. BMC Bioinformatics 11:227, 2010. PMID: 20441598

Mitchell C, Joyce AR, Piper JT, McKallip RJ, Fariss MW. Role of oxidative stress and MAPK signaling in reference moist smokeless tobacco-induced HOK-16B cell death. Toxicol Lett. 195(1):23-30, 2010. PMID: 20206247

Conrad TM, Joyce AR, Applebee MK, Barrett CL, Xie B, Gao Y, Palsson BO. Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short- term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations. Genome Biol. 10(10):R118, 2009.

Gianchandani EP, Joyce AR, Palsson BO, Papin JA. Functional States of the genome-scale Escherichia coli transcriptional regulatory system. PLoS Computational Biology, 5(6):e1000403, 2009.

Joyce AR and Palsson BO. In silico Genome-scale Metabolic Models: The Constraint-based Approach and its Applications. in Systems Biology and Synthetic Biology. P. Fu, M. Latterich and S. Panke, Eds. John Wiley & Brothers, Inc.: Hoboken, NJ; 2009. pp. 193-233.

Joyce AR and Palsson BO. Predicting gene essentiality using genome-scale in silico models. In: Osterman A and Gerdes S, editors. Gene essentiality at genome scale: protocols and bioinformatics. Totowa, NJ: Humana Press Inc.; 2008. pp. 433-57.

Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO. A genome-scale reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Molecular Systems Biology 3:121, 2007.

Hua Q, Joyce AR, Palsson BO, Fong SS. Metabolic characterization of Escherichia coli strains adapted to growth on lactate. Applied and Environmental Microbiology 73(14):4639-4647, 2007.

Joyce AR and Palsson BO. Toward whole cell modeling and simulation: comprehensive functional genomics through the constraint-based approach. In: Boshoff HI and Barry CE III, editors. Systems biological approaches in infectious diseases. Basel, Switzerland: Birkhauser Verlag; 2007. pp. 265, 267-309.

Allen TE, Price ND, Joyce AR, Palsson BO. Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization. PLoS Computational Biology 2(1):e2, 2006.

Gianchandani EP, Papin JA, Price ND, Joyce AR, Palsson BO. Matrix formalism to describe functional states of transcriptional regulatory systems. PLoS Comput Biol 2(8):e101 (2006).

Herring CD, Raghunathan A, Honisch C, Patel T, Applebee MK, Joyce AR, Albert TJ, Blattner FR, van den Boom D, Cantor CR, Palsson BO. Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nature Genetics 38(12):1406-1412, 2006.

Hua Q, Joyce AR, Fong SS, Palsson BO. Metabolic analysis of adaptive evolution for in silico-designed lactate-producing strains. Biotechnology and Bioengineering 95(5):992-1002, 2006.

Joyce AR and Palsson BO. The model organism as a system: integrating 'omics' data sets. Nature Reviews Molecular Cell Biology 7(3):198-210, 2006.

Joyce AR, Easterling K, Holtzman SG, Kuhar MJ. Modeling the onset of drug dependence: a consideration of the requirement for protein synthesis. Journal of Theoretical Biology 240(4):531-7, 2006.

Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S. Experimental and computational assessment of conditionally essential genes in Escherichia coli. Journal of Bacteriology 188(23):8259-8271, 2006.

Oh YK, Joyce AR, Palsson BO. Constraint-based genome-scale in silico models for systems biology. Asia-Pacific Biotech News 10:123-136, 2006.

Reed JL, Patel TR, Chen KH, Joyce AR, Applebee MK, Herring CD, Bui OT, Knight EM, Fong SS, Palsson BO. Systems approach to refining genome annotation. Proceedings of the National Academy of Sciences of the United States of America 103(46):17480-17484, 2006.

Fong SS, Joyce AR, Palsson BO. Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states. Genome Research 15(10):1365-1372, 2005.

Fong SS, Joyce AR, Palsson BO. The econometrics of evolution. Nature Chemical Biology 1(4):191-192, 2005.

Kimmel HL and Joyce AR. Dopamine transporters: structure-activity relationships and regulation in neurons. In: Dopamine receptors and transporters, 2nd edition. Vernier P, Sidhi A, Laruelle M. editors. New York (NY): Marcel Dekker, Inc; 2003. pp. 467-500.

Kuhar MJ and Joyce AR. Is the onset of psychoactive drug effects compatible with a protein-synthesis mechanism? Neuropsychopharmacology 28 Suppl 1: S94-97, 2003.

Kimmel HL, Joyce AR, Carroll FI, Kuhar MJ. Dopamine D1 and D2 receptors influence dopamine transporter synthesis and degradation in the rat. The Journal of Pharmacology and Experimental Therapeutics 298(1): 129-140, 2001.

Kuhar MJ and Joyce AR. Slow onset of CNS drugs: can changes in protein concentration account for the delay? Trends in Pharmacological Sciences 22(9):450-456, 2001.

Kuhar MJ, Joyce A, Dominguez G. Genes in drug abuse. Drug and Alcohol Dependence 62(3):157-162 2001.

Vrana PB, Matteson PG, Schmidt JV, Ingram RS, Joyce A, Prince KL, Dewey MJ, Tilghman SM. Genomic imprinting of a placental lactogen gene in Peromyscus. Development Genes and Evolution 211(11):523-532, 2001.