Publication List

Journals (* Authors initials are explained at bottom of page)

Authors Year Title Journal Volume Pages Abstract / Full Text


2003 Theoretical Design of a Gene Therapy To Prevent AIDS but Not Human Immunodeficiency Virus Type 1 Infection Journal of Virology 77(18) 10028-10036 [PDF-906kb]


2003 Motifs, modules and games in bacteria Current Opinion in Microbiology 6(2) 125-134 [PDF-273kb]

et al.

2003 The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models Bioinformatics 19(4) 524-531 [PDF-103kb]
CR, APA 2003 Stochastic Chemical Kinetics and the Quasi-Steady-State Assumption Journal of Chemical Physics 118(11) 4999-5010 [PDF-157kb]


2002 Control, exploitation and tolerance of intracellular noise Nature 420 231-238 [PDF-538kb]


2002 Determination of causal connectivities of species in reaction networks PNAS 99(9) 5816-5821 [Abstract]


2002 Signal Processing by Simple Chemical Systems Journal of Physical Chemistry A 106 10205-10221 [PDF-220kb]

et al.

2002 Functional profiling of the Saccharomyces cerevisiae genome Nature 418 387-391 [PDF-317kb]


2002 Genetic "Code": Representations and Dynamical Models of Genetic Components and Networks Annu. Rev. Genomics Hum. Genet. 3 341-369 [PDF-360kb]
DMW, APA 2002 15 minutes of fim: Control of Phase Variation in E. coli OMICS 6(1) 91-114 [PDF-783kb]
APA 2001 Synthetic Cell Biology Current Opinion in Biotechnology 12 638-644 [PDF-67kb]
CR, APA 2001 Control motifs for intracellular regulatory networks Annual Review of Biomedical Engineering 3 391-419 [PubMed]
MS, APA,JR 2001 On the deduction of chemical reaction pathways from measurements of time-series of concentrations. Chaos 11(1) 108-114


HHM, APA 2000 Towards a circuit engineering discipline. Current Biology 10(8) R318-20 [PubMed]
HHM, APA 1999 It's a noisy business! Genetic regulation at the nanomolar scale. Trends in Genetics 15(2) 65-69 [PubMed]
APA, JR, HHM 1998 Stochastic kinetic analysis of pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics 149(4) 1633-48


HHM, APA 1998 Simulation of prokaryotic genetic circuits Annual Review of Biophysics and Biomolecular Structure 27 199-224


CAS, APA, JR 1997 An endogenous calcium oscillator may control early embryonic division PNAS 94(4) 1194-1199 [PubMed]

APA, PDS, JR 1997 A test case of correlation metric construction of a reaction pathway from measurements Science 77(5330) 1275-1279
HHM, APA 1997 Stochastic mechanisms in gene expression PNAS 94(3) 814-819 [PubMed]

APA, JR 1995 Statistical construction of chemical reaction mechanisms from measured time series Journal of Physical Chemistry 99(3) 970-979 [PDF-3Mb]
APA, JR 1994 Computational functions in biochemical reaction networks Biophysical Journal 67(2) 560-578 [PubMed]
APA, DYC 1992 An algorithm for protein engineering PNAS 89(16) 7811-7815 [PubMed]
APA, DYC 1992 Optimizing nucleotide mixtures to encode specific subsets of amino acids for semi-random mutagenesis Biotechnology 10(3) 297-300 [PubMed]
APA, ..., DYC 1990 Applications of imaging spectroscopy in molecular biology. II. Colony screening based on absorption spectra. Biotechnology 8(8) 746-749 [PubMed]

BookChapters (* Authors initials are explained at bottom of page)

Authors Year Title Book Editors ISBN Info
APA 2000 Signal Processing in Biochemical Reaction Networks Self-Organized Biological Dynamics and Nonlinear Control J. Walleczek 0521-6243-63 [Amazon]
APA, DCY 1992 Digital Imaging Spectroscopy The Photosynthetic Reaction Center J. Deisenhofer, J.R. Norris 0122-0866-00 [Amazon]

Conference Proceedings (* Authors initials are explained at bottom of page)

Authors Year Title Book Editors ISBN Info
APA, ..., DCY 1992 Recursive Ensemble Mutagenesis: A Combinatorial Optimization Technique For Protein Engineering Parallel Problem Solving from Nature II. Proceedings of the Second International Conference on Parallel Problem Solving from Nature. R. Maenner, B. Manderick 0521-6243-63 [Amazon]


Initials Author
APA Adam P. Arkin
AG Alex Gilman
CAS Craig A. Swanson
CR Christopher Rao
DCY Douglas C. Youvan
DMW Denise Wolf
DVS David V. Schaffer
GG Guri Giaever
HHM Harley H. McAdams
JLK Jay L. Kasberger
JR John Ross
LSW Leor S. Weinberger
MH Michael Hucka
MS Michael Samoilov
PDS Pei-Dong Shen
PF Patrick Flaherty
WV William Vance


Department of Bioengineering, University of California, Berkeley, CA 94720
Physical Biosciences Division, 1 Cyclotron Road, MS Stanley, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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© Adam Arkin, 2000,. All Rights Reserved


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