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Items: 1 to 20 of 22

1.

Effects of genetic variation on the E. coli host-circuit interface.

Cardinale S, Joachimiak MP, Arkin AP.

Cell Rep. 2013 Jul 25;4(2):231-7. doi: 10.1016/j.celrep.2013.06.023. Epub 2013 Jul 18. Review.

2.

Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution.

Zhou A, Baidoo E, He Z, Mukhopadhyay A, Baumohl JK, Benke P, Joachimiak MP, Xie M, Song R, Arkin AP, Hazen TC, Keasling JD, Wall JD, Stahl DA, Zhou J.

ISME J. 2013 Sep;7(9):1790-802. doi: 10.1038/ismej.2013.60. Epub 2013 Apr 11.

3.

Deletion of the Desulfovibrio vulgaris carbon monoxide sensor invokes global changes in transcription.

Rajeev L, Hillesland KL, Zane GM, Zhou A, Joachimiak MP, He Z, Zhou J, Arkin AP, Wall JD, Stahl DA.

J Bacteriol. 2012 Nov;194(21):5783-93. doi: 10.1128/JB.00749-12. Epub 2012 Aug 17.

4.

Functional responses of methanogenic archaea to syntrophic growth.

Walker CB, Redding-Johanson AM, Baidoo EE, Rajeev L, He Z, Hendrickson EL, Joachimiak MP, Stolyar S, Arkin AP, Leigh JA, Zhou J, Keasling JD, Mukhopadhyay A, Stahl DA.

ISME J. 2012 Nov;6(11):2045-55. doi: 10.1038/ismej.2012.60. Epub 2012 Jun 28.

5.

Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state.

Clark ME, He Z, Redding AM, Joachimiak MP, Keasling JD, Zhou JZ, Arkin AP, Mukhopadhyay A, Fields MW.

BMC Genomics. 2012 Apr 16;13:138. doi: 10.1186/1471-2164-13-138.

6.

Mutual information analysis reveals coevolving residues in Tat that compensate for two distinct functions in HIV-1 gene expression.

Dey SS, Xue Y, Joachimiak MP, Friedland GD, Burnett JC, Zhou Q, Arkin AP, Schaffer DV.

J Biol Chem. 2012 Mar 9;287(11):7945-55. doi: 10.1074/jbc.M111.302653. Epub 2012 Jan 17.

7.

Application of phenotypic microarrays to environmental microbiology.

Borglin S, Joyner D, DeAngelis KM, Khudyakov J, D'haeseleer P, Joachimiak MP, Hazen T.

Curr Opin Biotechnol. 2012 Feb;23(1):41-8. doi: 10.1016/j.copbio.2011.12.006. Epub 2012 Jan 2. Review.

8.

Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough.

Zhou A, Chen YI, Zane GM, He Z, Hemme CL, Joachimiak MP, Baumohl JK, He Q, Fields MW, Arkin AP, Wall JD, Hazen TC, Zhou J.

Appl Environ Microbiol. 2012 Feb;78(4):1168-77. doi: 10.1128/AEM.05666-11. Epub 2011 Dec 9.

9.

Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough.

Chhabra SR, Joachimiak MP, Petzold CJ, Zane GM, Price MN, Reveco SA, Fok V, Johanson AR, Batth TS, Singer M, Chandonia JM, Joyner D, Hazen TC, Arkin AP, Wall JD, Singh AK, Keasling JD.

PLoS One. 2011;6(6):e21470. doi: 10.1371/journal.pone.0021470. Epub 2011 Jun 28.

10.

Shewanella oneidensis MR-1 sensory box protein involved in aerobic and anoxic growth.

Sundararajan A, Kurowski J, Yan T, Klingeman DM, Joachimiak MP, Zhou J, Naranjo B, Gralnick JA, Fields MW.

Appl Environ Microbiol. 2011 Jul;77(13):4647-56. doi: 10.1128/AEM.03003-10. Epub 2011 May 20.

11.

An SF1 affinity model to identify branch point sequences in human introns.

Pastuszak AW, Joachimiak MP, Blanchette M, Rio DC, Brenner SE, Frankel AD.

Nucleic Acids Res. 2011 Mar;39(6):2344-56. doi: 10.1093/nar/gkq1046. Epub 2010 Nov 10.

12.

Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough.

Zhou A, He Z, Redding-Johanson AM, Mukhopadhyay A, Hemme CL, Joachimiak MP, Luo F, Deng Y, Bender KS, He Q, Keasling JD, Stahl DA, Fields MW, Hazen TC, Arkin AP, Wall JD, Zhou J.

Environ Microbiol. 2010 Oct;12(10):2645-57. doi: 10.1111/j.1462-2920.2010.02234.x.

PMID:
20482586
13.

Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation.

He Z, Zhou A, Baidoo E, He Q, Joachimiak MP, Benke P, Phan R, Mukhopadhyay A, Hemme CL, Huang K, Alm EJ, Fields MW, Wall J, Stahl D, Hazen TC, Keasling JD, Arkin AP, Zhou J.

Appl Environ Microbiol. 2010 Mar;76(5):1574-86. doi: 10.1128/AEM.02141-09. Epub 2009 Dec 28.

14.

MicrobesOnline: an integrated portal for comparative and functional genomics.

Dehal PS, Joachimiak MP, Price MN, Bates JT, Baumohl JK, Chivian D, Friedland GD, Huang KH, Keller K, Novichkov PS, Dubchak IL, Alm EJ, Arkin AP.

Nucleic Acids Res. 2010 Jan;38(Database issue):D396-400. doi: 10.1093/nar/gkp919. Epub 2009 Nov 11.

15.

Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation.

Elias DA, Mukhopadhyay A, Joachimiak MP, Drury EC, Redding AM, Yen HC, Fields MW, Hazen TC, Arkin AP, Keasling JD, Wall JD.

Nucleic Acids Res. 2009 May;37(9):2926-39. doi: 10.1093/nar/gkp164. Epub 2009 Mar 17.

16.

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.

J Bacteriol. 2007 Dec;189(24):8944-52. Epub 2007 Oct 5.

17.

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.

J Bacteriol. 2007 Aug;189(16):5996-6010. Epub 2007 Jun 1.

18.

The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families.

Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, Joachimiak MP, van Belle C, Chandonia JM, Soergel DA, Zhai Y, Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A, Eisenberg D, Dixon JE, Taylor SS, Strausberg RL, Frazier M, Venter JC.

PLoS Biol. 2007 Mar;5(3):e16.

19.

JColorGrid: software for the visualization of biological measurements.

Joachimiak MP, Weisman JL, May BCh.

BMC Bioinformatics. 2006 Apr 27;7:225.

20.

Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray.

Bozdech Z, Zhu J, Joachimiak MP, Cohen FE, Pulliam B, DeRisi JL.

Genome Biol. 2003;4(2):R9. Epub 2003 Jan 31.

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