Epernicus: Adam P. Arkin, Ph.D.

Adam P. Arkin, Ph.D.

Position:
Professor

Bioengineering

University of California, Berkeley (Berkeley, CA)
Degrees:

Ph.D., Chemistry, Massachusetts Institute of Technology (Cambridge, MA)

B.A., Chemistry, Carleton College (Northfield, MN)
Past Advisors:

Harley H. McAdams (as Post Doctoral Fellow)

Lucy Shapiro (as Post Doctoral Fellow)

John Ross (as Post Doctoral Fellow)

Keith A. Nelson (as Graduate Student - Ph.D.)

Douglas C. Youvan (as Graduate Student - Ph.D.)
Research:

Communities:

Adam Arkin's Genealogy

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Adam Arkin's Publications (79)

Setting the standard in synthetic biology.
Arkin A

Nature biotechnology. 2008 Jul;26(7):771-4
Modularity of stress response evolution.
Singh AH, Wolf DM, Wang P, Arkin AP

Proceedings of the National Academy of Sciences of the United States of America. 2008 May 27;105(21):7500-5
Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli.
Price MN, Dehal PS, Arkin AP

Genome biology. 2008 Jan 7;9(1):R4
Identification of genes involved in the toxic response of Saccharomyces cerevisiae against iron and copper overload by parallel analysis of deletion mutants.
Jo WJ, Loguinov A, Chang M, Wintz H, Nislow C, Arkin AP, Giaever G, Vulpe CD

Toxicological sciences : an official journal of the Society of Toxicology. 2008 Jan;101(1):140-51
Design and construction of a double inversion recombination switch for heritable sequential genetic memory.
Ham TS, Lee SK, Keasling JD, Arkin AP

PLoS ONE. 2008;3(7):e2815
Memory in microbes: quantifying history-dependent behavior in a bacterium.
Wolf DM, Fontaine-Bodin L, Bischofs I, Price G, Keasling J, Arkin AP

PLoS ONE. 2008;3(2):e1700
Response of Desulfovibrio vulgaris to alkaline stress.
Stolyar S, He Q, Joachimiak MP, He Z, Yang ZK, Borglin SE, Joyner DC, Huang K, Alm E, Hazen TC, Zhou J, Wall JD, Arkin AP, Stahl DA

Journal of bacteriology. 2007 Dec;189(24):8944-52
A mechanical explanation for cytoskeletal rings and helices in bacteria.
Andrews SS, Arkin AP

Biophysical journal. 2007 Sep 15;93(6):1872-84
Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough.
Bender KS, Yen HC, Hemme CL, Yang Z, He Z, He Q, Zhou J, Huang KH, Alm EJ, Hazen TC, Arkin AP, Wall JD

Applied and environmental microbiology. 2007 Sep;73(17):5389-400
Orthologous transcription factors in bacteria have different functions and regulate different genes.
Price MN, Dehal PS, Arkin AP

PLoS computational biology. 2007 Sep;3(9):1739-50
Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough.
Mukhopadhyay A, Redding AM, Joachimiak MP, Arkin AP, Borglin SE, Dehal PS, Chakraborty R, Geller JT, Hazen TC, He Q, Joyner DC, Martin VJ, Wall JD, Yang ZK, Zhou J, Keasling JD

Journal of bacteriology. 2007 Aug;189(16):5996-6010
Systems biology: a switch for sex.
Andrews SS, Arkin AP

Current biology : CB. 2007 Jun 5;17(11):R410-2
RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes.
Kazakov AE, Cipriano MJ, Novichkov PS, Minovitsky S, Vinogradov DV, Arkin A, Mironov AA, Gelfand MS, Dubchak I

Nucleic acids research. 2007 Jan;35(Database issue):D407-12
Environmental signal integration by a modular AND gate.
Anderson JC, Voigt CA, Arkin AP

Molecular systems biology. 2007;3:133
Global analysis of host response to induction of a latent bacteriophage.
Osterhout RE, Figueroa IA, Keasling JD, Arkin AP

BMC microbiology. 2007;7:82
From fluctuations to phenotypes: the physiology of noise.
Samoilov MS, Price G, Arkin AP

Science's STKE : signal transduction knowledge environment. 2006 Dec 19;2006(366):re17
The evolution of two-component systems in bacteria reveals different strategies for niche adaptation.
Alm E, Huang K, Arkin A

PLoS computational biology. 2006 Nov 3;2(11):e143
Deviant effects in molecular reaction pathways.
Samoilov MS, Arkin AP

Nature biotechnology. 2006 Oct;24(10):1235-40
Morphology matters in immune cell chemotaxis: membrane asymmetry affects amplification.
Onsum MD, Wong K, Herzmark P, Bourne HR, Arkin AP

Physical biology. 2006 Sep;3(3):190-9
Temporal transcriptomic analysis as Desulfovibrio vulgaris Hildenborough transitions into stationary phase during electron donor depletion.
Clark ME, He Q, He Z, Huang KH, Alm EJ, Wan XF, Hazen TC, Arkin AP, Wall JD, Zhou JZ, Fields MW

Applied and environmental microbiology. 2006 Aug;72(8):5578-88
Simulating cell biology.
Andrews SS, Arkin AP

Current biology : CB. 2006 Jul 25;16(14):R523-7
Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis.
He Q, Huang KH, He Z, Alm EJ, Fields MW, Hazen TC, Arkin AP, Wall JD, Zhou J

Applied and environmental microbiology. 2006 Jun;72(6):4370-81
Genomics for environmental microbiology.
Deutschbauer AM, Chivian D, Arkin AP

Current opinion in biotechnology. 2006 Jun;17(3):229-35
Model discrimination using data collaboration.
Feeley R, Frenklach M, Onsum M, Russi T, Arkin A, Packard A

The journal of physical chemistry. A. 2006 Jun 1;110(21):6803-13
Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach.
Mukhopadhyay A, He Z, Alm EJ, Arkin AP, Baidoo EE, Borglin SC, Chen W, Hazen TC, He Q, Holman HY, Huang K, Huang R, Joyner DC, Katz N, Keller M, Oeller P, Redding A, Sun J, Wall J, Wei J, Yang Z, Yen HC, Zhou J, Keasling JD

Journal of bacteriology. 2006 Jun;188(11):4068-78

Adam P. Arkin, Ph.D.

Professor

Adam Arkin's Genealogy

Adam Arkin's Publications (79)

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