Joachimiak, Marcin

TitleSoftware Developer 3
InstitutionLawrence Berkeley National Lab
DepartmentEnviron Genomics & Systems Bio
Address1 Cyclotron Road
Berkeley CA 94720
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Cardinale S, Joachimiak M, Arkin AP. Effects of genetic variation on the E. coli host-circuit interface. Cell Rep. 2013 Jul 25; 4(2):231-7. PMID: 23871664.
      View in: PubMed
    2. Zhou A, Baidoo E, He Z, Mukhopadhyay A, Baumohl JK, Benke P, Joachimiak M, Xie M, Song R, Arkin AP, Hazen TC, Keasling JD, Wall JD, Stahl DA, Zhou J. Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution. ISME J. 2013 Sep; 7(9):1790-802. PMID: 23575373; PMCID: PMC3749499.
    3. Rajeev L, Hillesland KL, Zane GM, Zhou A, Joachimiak M, He Z, Zhou J, Arkin AP, Wall JD, Stahl DA. Deletion of the Desulfovibrio vulgaris carbon monoxide sensor invokes global changes in transcription. J Bacteriol. 2012 Nov; 194(21):5783-93. PMID: 22904289; PMCID: PMC3486112.
    4. Walker CB, Redding-Johanson AM, Baidoo EE, Rajeev L, He Z, Hendrickson EL, Joachimiak M, Stolyar S, Arkin AP, Leigh JA, Zhou J, Keasling JD, Mukhopadhyay A, Stahl DA. Functional responses of methanogenic archaea to syntrophic growth. ISME J. 2012 Nov; 6(11):2045-55. PMID: 22739494; PMCID: PMC3475374.
    5. Clark ME, He Z, Redding AM, Joachimiak M, Keasling JD, Zhou JZ, Arkin AP, Mukhopadhyay A, Fields MW. Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state. BMC Genomics. 2012 Apr 16; 13:138. PMID: 22507456; PMCID: PMC3431258.
    6. Dey SS, Xue Y, Joachimiak M, Friedland GD, Burnett JC, Zhou Q, Arkin AP, Schaffer DV. Mutual information analysis reveals coevolving residues in Tat that compensate for two distinct functions in HIV-1 gene expression. J Biol Chem. 2012 Mar 09; 287(11):7945-55. PMID: 22253435; PMCID: PMC3318752.
    7. Borglin S, Joyner D, DeAngelis KM, Khudyakov J, D'haeseleer P, Joachimiak M, Hazen T. Application of phenotypic microarrays to environmental microbiology. Curr Opin Biotechnol. 2012 Feb; 23(1):41-8. PMID: 22217654.
      View in: PubMed
    8. Zhou A, Chen YI, Zane GM, He Z, Hemme CL, Joachimiak M, Baumohl JK, He Q, Fields MW, Arkin AP, Wall JD, Hazen TC, Zhou J. Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough. Appl Environ Microbiol. 2012 Feb; 78(4):1168-77. PMID: 22156435; PMCID: PMC3273024.
    9. Chhabra SR, Joachimiak M, 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. Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough. PLoS One. 2011; 6(6):e21470. PMID: 21738675; PMCID: PMC3125180.
    10. Pastuszak AW, Joachimiak M, Blanchette M, Rio DC, Brenner SE, Frankel AD. An SF1 affinity model to identify branch point sequences in human introns. Nucleic Acids Res. 2011 Mar; 39(6):2344-56. PMID: 21071404; PMCID: PMC3064769.
    11. Zhou A, He Z, Redding-Johanson AM, Mukhopadhyay A, Hemme CL, Joachimiak M, Luo F, Deng Y, Bender KS, He Q, Keasling JD, Stahl DA, Fields MW, Hazen TC, Arkin AP, Wall JD, Zhou J. Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough. Environ Microbiol. 2010 Oct; 12(10):2645-57. PMID: 20482586.
      View in: PubMed
    12. He Q, He Z, Joyner DC, Joachimiak M, Price MN, Yang ZK, Yen HC, Hemme CL, Chen W, Fields MM, Stahl DA, Keasling JD, Keller M, Arkin AP, Hazen TC, Wall JD, Zhou J. Impact of elevated nitrate on sulfate-reducing bacteria: a comparative study of Desulfovibrio vulgaris. ISME J. 2010 Nov; 4(11):1386-97. PMID: 20445634.
      View in: PubMed
    13. He Z, Zhou A, Baidoo E, He Q, Joachimiak M, 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. Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation. Appl Environ Microbiol. 2010 Mar; 76(5):1574-86. PMID: 20038696; PMCID: PMC2832388.
    14. Dehal PS, Joachimiak M, Price MN, Bates JT, Baumohl JK, Chivian D, Friedland GD, Huang KH, Keller K, Novichkov PS, Dubchak IL, Alm EJ, Arkin AP. MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res. 2010 Jan; 38(Database issue):D396-400. PMID: 19906701; PMCID: PMC2808868.
    15. Yang Y, Harris DP, Luo F, Xiong W, Joachimiak M, Wu L, Dehal P, Jacobsen J, Yang Z, Palumbo AV, Arkin AP, Zhou J. Snapshot of iron response in Shewanella oneidensis by gene network reconstruction. BMC Genomics. 2009 Mar 25; 10:131. PMID: 19321007; PMCID: PMC2667191.
    16. Elias DA, Mukhopadhyay A, Joachimiak M, Drury EC, Redding AM, Yen HC, Fields MW, Hazen TC, Arkin AP, Keasling JD, Wall JD. Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation. Nucleic Acids Res. 2009 May; 37(9):2926-39. PMID: 19293273; PMCID: PMC2685097.
    17. Stolyar S, He Q, Joachimiak M, He Z, Yang ZK, Borglin SE, Joyner DC, Huang K, Alm E, Hazen TC, Zhou J, Wall JD, Arkin AP, Stahl DA. Response of Desulfovibrio vulgaris to alkaline stress. J Bacteriol. 2007 Dec; 189(24):8944-52. PMID: 17921288; PMCID: PMC2168612.
    18. Mukhopadhyay A, Redding AM, Joachimiak M, 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. Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough. J Bacteriol. 2007 Aug; 189(16):5996-6010. PMID: 17545284; PMCID: PMC1952033.
    19. 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 M, 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. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol. 2007 Mar; 5(3):e16. PMID: 17355171; PMCID: PMC1821046.
    20. Joachimiak M, Weisman JL, May BCh. JColorGrid: software for the visualization of biological measurements. BMC Bioinformatics. 2006 Apr 27; 7:225. PMID: 16640789; PMCID: PMC1479842.
    21. Bozdech Z, Zhu J, Joachimiak M, Cohen FE, Pulliam B, DeRisi JL. Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biol. 2003; 4(2):R9. PMID: 12620119; PMCID: PMC151308.
    22. Joachimiak M, Cohen FE. JEvTrace: refinement and variations of the evolutionary trace in JAVA. Genome Biol. 2002; 3(12):RESEARCH0077. PMID: 12537566; PMCID: PMC151179.

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