Marcin P. Joachimiak, Ph.D. - Publications

Affiliations: 
University of California, San Francisco, San Francisco, CA 
Area:
protein folding

28 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2013 Cardinale S, Joachimiak MP, Arkin AP. Effects of genetic variation on the E. coli host-circuit interface. Cell Reports. 4: 231-7. PMID 23871664 DOI: 10.1016/j.celrep.2013.06.023  0.92
2013 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. Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution. The Isme Journal. 7: 1790-802. PMID 23575373 DOI: 10.1038/ismej.2013.60  0.92
2012 Rajeev L, Hillesland KL, Zane GM, Zhou A, Joachimiak MP, He Z, Zhou J, Arkin AP, Wall JD, Stahl DA. Deletion of the Desulfovibrio vulgaris carbon monoxide sensor invokes global changes in transcription. Journal of Bacteriology. 194: 5783-93. PMID 22904289 DOI: 10.1128/JB.00749-12  0.92
2012 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. Functional responses of methanogenic archaea to syntrophic growth. The Isme Journal. 6: 2045-55. PMID 22739494 DOI: 10.1038/ismej.2012.60  0.92
2012 Clark ME, He Z, Redding AM, Joachimiak MP, 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. 13: 138. PMID 22507456 DOI: 10.1186/1471-2164-13-138  0.92
2012 Dey SS, Xue Y, Joachimiak MP, 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. The Journal of Biological Chemistry. 287: 7945-55. PMID 22253435 DOI: 10.1074/jbc.M111.302653  0.92
2012 Borglin S, Joyner D, DeAngelis KM, Khudyakov J, D'haeseleer P, Joachimiak MP, Hazen T. Application of phenotypic microarrays to environmental microbiology. Current Opinion in Biotechnology. 23: 41-8. PMID 22217654 DOI: 10.1016/j.copbio.2011.12.006  0.92
2012 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. Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough. Applied and Environmental Microbiology. 78: 1168-77. PMID 22156435 DOI: 10.1128/AEM.05666-11  0.92
2011 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, et al. Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough. Plos One. 6: e21470. PMID 21738675 DOI: 10.1371/journal.pone.0021470  0.92
2011 Sundararajan A, Kurowski J, Yan T, Klingeman DM, Joachimiak MP, Zhou J, Naranjo B, Gralnick JA, Fields MW. Shewanella oneidensis MR-1 sensory box protein involved in aerobic and anoxic growth. Applied and Environmental Microbiology. 77: 4647-56. PMID 21602393 DOI: 10.1128/AEM.03003-10  0.92
2011 Pastuszak AW, Joachimiak MP, Blanchette M, Rio DC, Brenner SE, Frankel AD. An SF1 affinity model to identify branch point sequences in human introns. Nucleic Acids Research. 39: 2344-56. PMID 21071404 DOI: 10.1093/nar/gkq1046  0.92
2010 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, et al. Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough. Environmental Microbiology. 12: 2645-57. PMID 20482586 DOI: 10.1111/j.1462-2920.2010.02234.x  0.92
2010 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, et al. Impact of elevated nitrate on sulfate-reducing bacteria: a comparative study of Desulfovibrio vulgaris. The Isme Journal. 4: 1386-97. PMID 20445634 DOI: 10.1038/ismej.2010.59  0.92
2010 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, et al. Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation. Applied and Environmental Microbiology. 76: 1574-86. PMID 20038696 DOI: 10.1128/AEM.02141-09  0.92
2010 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. MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Research. 38: D396-400. PMID 19906701 DOI: 10.1093/nar/gkp919  0.92
2009 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. 10: 131. PMID 19321007 DOI: 10.1186/1471-2164-10-131  0.92
2009 Elias DA, Mukhopadhyay A, Joachimiak MP, 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 Research. 37: 2926-39. PMID 19293273 DOI: 10.1093/nar/gkp164  0.92
2007 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. Response of Desulfovibrio vulgaris to alkaline stress. Journal of Bacteriology. 189: 8944-52. PMID 17921288 DOI: 10.1128/JB.00284-07  0.92
2007 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, et al. Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough. Journal of Bacteriology. 189: 5996-6010. PMID 17545284 DOI: 10.1128/JB.00368-07  0.92
2007 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, et al. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. Plos Biology. 5: e16. PMID 17355171 DOI: 10.1371/journal.pbio.0050016  0.92
2006 Joachimiak MP, Weisman JL, May BCh. JColorGrid: software for the visualization of biological measurements. Bmc Bioinformatics. 7: 225. PMID 16640789 DOI: 10.1186/1471-2105-7-225  0.92
2003 Bozdech Z, Zhu J, Joachimiak MP, Cohen FE, Pulliam B, DeRisi JL. Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biology. 4: R9. PMID 12620119  0.92
2002 Joachimiak MP, Cohen FE. JEvTrace: refinement and variations of the evolutionary trace in JAVA. Genome Biology. 3: RESEARCH0077. PMID 12537566  0.92
2001 Joachimiak MP, Chang C, Rosenthal PJ, Cohen FE. The impact of whole genome sequence data on drug discovery--a malaria case study. Molecular Medicine (Cambridge, Mass.). 7: 698-710. PMID 11713369  0.92
2000 Goh CS, Bogan AA, Joachimiak M, Walther D, Cohen FE. Co-evolution of proteins with their interaction partners. Journal of Molecular Biology. 299: 283-93. PMID 10860738 DOI: 10.1006/jmbi.2000.3732  0.92
1999 Gerloff DL, Cannarozzi GM, Joachimiak M, Cohen FE, Schreiber D, Benner SA. Evolutionary, mechanistic, and predictive analyses of the hydroxymethyldihydropterin pyrophosphokinase family of proteins. Biochemical and Biophysical Research Communications. 254: 70-6. PMID 9920734 DOI: 10.1006/bbrc.1998.9884  0.92
1998 Gerloff DL, Joachimiak M, Cohen FE, Cannarozzi GM, Chamberlin SG, Benner SA. Structure prediction in a post-genomic environment: a secondary and tertiary structural model for the initiation factor 5A family. Biochemical and Biophysical Research Communications. 251: 173-81. PMID 9790926 DOI: 10.1006/bbrc.1998.9198  0.92
1997 Joachimiak M, Tevzadze G, Podkowinski J, Haselkorn R, Gornicki P. Wheat cytosolic acetyl-CoA carboxylase complements an ACC1 null mutation in yeast. Proceedings of the National Academy of Sciences of the United States of America. 94: 9990-5. PMID 11038571 DOI: 10.1073/pnas.94.18.9990  0.92
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