4th year Graduate Student

Program in Bioinformatics

My research currently focuses on modeling transcriptional regulatory networks and studying adaptive evolution in E. coli through the analysis and integration of so-called 'omics data sets. When not in the lab you can find me out and about enjoying San Diego with my better half (Kerri), seeking athletic glory through pickup soccer, rugby, and intramurals, or cheering wicked hard for the Sawx, B's, C's, and Pat's.

Education

University of California, San Diego

Ph.D Candidate, Bioinformatics Program

Princeton University

A.B. in Molecular Biology, June 1999 (Cum Laude)

Honors and Activities

Princeton University

Alumni Schools Committee, Applicant Interviewer, 2005-2006

NSF Graduate Research Fellowship, Honorable Mention, 2004

NIH Training Grant, 2002-2003

Sigma Xi, The Scientific Research Society, 1999-2001

Teaching Experience

BE211 - Systems Biology I: Biological Components, Teaching Assistant

BE212 - Systems Biology II: Network Reconstruction and Analysis, Teaching Assistant

BE213 - Systems Biology III: Network Dynamics, Webmaster/Course Assistant

Coursework

Bioinformatics: Biological Data Modeling and Analysis, Sequence and Structure Analysis, Genome-scale Modeling and Analysis.

Biology: Biochemical Techniques, Biochemistry, Cell Biology, Genetics, Molecular Biology, Molecular Evolution, Post-Genomics Biology.

Chemistry: General Chemistry, Organic Chemistry.

Computer Science: Advanced Data Structures, Algorithm Design and Analysis.

Engineering: Computational Biomechanics, Thermodynamics.

Mathematics and Statistics: Linear Algebra, Multivariate Calculus, Numerical Methods, ODEs, Mathematical Statistics, Statistical Methods in Bioinformatics.

Publications

Articles

Reed JL, Patel TR, Chen KH, Joyce AR, Applebee MK, Herring CD, Bui OT, Knight EM, Fong SS and Palsson BØ (2006) "Systems approach to refining genome annotation" Proc Natl Acad Sci U S A 103(46): 17480-4.

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

Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BØ and Agarwalla S. (2006) "Experimental and computational assessment of conditionally essential genes in Escherichia coli" J Bacteriol 188(23): 8259-71.

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

Joyce AR, Palsson BØ (2006) "The model organism as a system: integrating 'omics' data sets" Nat Rev Mol Cell Biol 7(3):198-210.

Oh YK, Joyce AR, and Palsson BØ (2006) "Constraint-based Genome-Scale In Silico Models for Systems Biology" Asia-Pacific Biotech News 10:123-36.

Allen TE, Price ND, Joyce AR, Palsson BØ (2006) "Long-Range Periodic Patterns in Microbial Genomes Indicate Significant Multi-Scale Chromosomal Organization" PLoS Comput Biol, 2(1):e2.

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

Fong SS, Joyce AR, Palsson BØ (2005) "The Econometrics of Evolution" Nat Chem Biol, 1(4):191-2.

Fong SS, Joyce AR, Palsson BØ (2005) "Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states" Genome Res., 15(10):1365-72.

###Book Chapters Joyce AR and Palsson BØ (2007) "Toward whole cell modeling and simulation: comprehensive functional genomics through the constraint-based approach". in Systems Biological Approaches in Infectious Diseases. H. I. Boshoff and C. E. Barry III, Eds. Basel, Switzerland, Birkhauser Verlag. p. 265, 267-309.

Conferences

“Probing the genotype-phenotype relationship in E. coli strains adapted to growth on glycerol”.

Poster at the 14th Annual International Microbial Genomics Conference, September 2006, Lake Arrowhead, CA.

Joyce AR, Maggay A, Herring CD, Zhang J, Landick R, and Palsson BØ.

“Modeling cellular pathways and applications to Thermotoga maritima ”.

Invited speaker at the Joint Center for Structural Genomics Annual Meeting. The Scripps Research Institute, April 2006, San Diego, CA.

Joyce AR and Palsson BØ.

"Adaptive evolution of E. coli on either glycerol or lactate leads to convergent, generalist phenotypes"

Poster at 2nd International E. coli Alliance Conference on Systems Biology, Banff, Alberta (2004)

Joyce AR, Fong SS, Palsson BØ

"Adaptive evolution of E. coli on lactate leads to convergent, generalist phenotypes"

Poster at RECOMB Conference, San Diego, CA (2004)

Joyce AR, Fong SS, Palsson BØ

Past Life

 Articles

Joyce AR, Easterling K, Holtzman SG, Kuhar MJ (2005) "Modeling the onset of drug dependence: A consideration of the requirement for protein synthesis." J Theor Biol 240(4): 531-7.

Kuhar MJ, Joyce AR (2003) "Is the Onset of Psychoactive Drug Effects Compatible with a Protein-Synthesis Mechanism?" Neuropsychopharmacology 28: S94-7.

Kimmel HL, Joyce AR, Carroll FI, Kuhar MJ (2001) "Dopamine D1 and D2 Receptors Influence Dopamine Transporter Synthesis and Degradation in the Rat." Journal of Pharmacology and Experimental Therapeutics, 298:129-140.

Kuhar MJ, Joyce AR (2001) "Slow Onset of CNS Drugs: Can Changes in Protein Concentration Account for the Delay?" Trends in Pharmacological Sciences, 22:450-456.

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

Vrana PB, Matteson PG, Schmidt JV, Ingram RS, Joyce A, Prince KL, Dewey MJ, Tilghman SM (2001) "Genomic Imprinting of a Placental Lactogen Gene in Peromyscus." Dev Genes Evol, '211(11):'532-32.

Book Chapters

Kimmel, HL, Joyce, AR (2003) "Dopamine Transporters: Structure-Activity Relationships and Regulation in Neurons" Dopamine Receptors and Transporters, 2nd Edition. Eds. P. Vernier, A. Sidhi, and M. Laruelle. New York: Marcel Dekker, Inc., pp. 467-500.

Conferences

Dopamine Transporter Protein Synthesis and Degradation in Rat Striatum and Nucleus Accumbens.

Poster at Society for Neuroscience Annual Meeting, Orlando, FL. (2002)

Kuhar MJ, Kimmel HL, Joyce AR, Carroll FI

A Model for the Time Courses of Levels of Sequentially Produced Proteins.

Poster at Society for Neuroscience Annual Meeting, San Diego, CA. (2001)

Joyce AR, Kuhar MJ

Slow Onset of Addicting Drugs: Can Changes in Levels of Proteins Account for the Delay.

Poster at College on Problems of Drug Dependence Annual Meeting, Scottsdale, AZ. (2001) Joyce AR, Kuhar MJ

Dopamine Receptor Agonists and Antagonists Alter DAT Turnover in the Striatum and Nucleus Accumbens.

College on Problems of Drug Dependence Annual Meeting, San Juan, PR. (2000) Kimmel HL, Joyce AR, Carroll FI, Kuhar MJ

Contact Information

Email Address: ajoyce@ucsd.edu

Phone: (858)822-1144

Mailing Address: 9500 Gilman Drive Mail Code 0412 La Jolla, CA 92093-0412