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• Price, M.N. et. al. FastTree 2 -- Approximately Maximum-Likelihood Trees for Large Alignments PLoS ONE 2010, 5(3):e9490.
• Dehal, P.S. et. al. MicrobesOnline: an integrated portal for comparative and functional genomics Nucleic Acids Res. 2009 Nov 11.
• D. Chivian, E. L. Brodie, E. J. Alm, et. al. Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth. Science 2008 322:275-278.
• Price, M.N., Dehal, P.S., and Arkin, A.P. FastTree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix. Molecular Biology and Evolution 26:1641-1650
• Price, M.N., Dehal, P.S., and Arkin, A.P. FastBLAST: Homology relationships for millions of proteins. PLoS ONE 2008 3(10): e3589.
• Price, M.N., Dehal, P.S., and Arkin, A.P. Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli. Genome Biology 2008 9:R4.
• Price, M.N., Dehal, P.S., and Arkin, A.P. Orthologous transcription factors in bacteria have different functions and regulate different genes. PLoS Computational Biology 2007, 3(9): e175.
• Alm E., Huang, K., and Arkin, A. The Evolution of Two-Component Systems in Bacteria Reveals Different Strategies for Niche Adaptation. PLoS Computational Biology 2006 2(11): e143.
• M.N. Price, A.P. Arkin, E.J. Alm. The Life-cycle of Operons. PLoS Genetics 2(6):e96.
• A. Mukhopadhyay et al. Salt Stress in Desulfovibrio vulgaris Hildenborough: an Integrated Genomics Approach. J Bacteriol. 2006 Jun;188(11):4068-78.
• M.N. Price, E.J. Alm, A.P. Arkin. The Histidine Operon Is Ancient. J Mol Evol. 2006 Apr 11.
• S.R. Chhabra et al. Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough. J Bacteriol. 2006 Mar;188(5):1817-28.
• A.B. Leaphart et al. Transcriptome profiling of Shewanella oneidensis gene expression following exposure to acidic and alkaline pH. J Bacteriol. 2006 Feb;188(4):1633-42.
• M.N. Price, A.P. Arkin, E.J. Alm. OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments. BMC Bioinformatics. 2006 Jan 13;7(1):19
• S.D Brown et al. Cellular Response of Shewanella oneidensis to Strontium Stress. Appl. Environ. Microbiol. 2006 Jan;72(1):890-900
• D.A. Rodionov, I. Dubchak, A. Arkin, E. Alm, M.S. Gelfand. Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks. PLoS Comput Biol. 2005 Oct;1(5):e55.
• E.J. Alm, K.H. Huang, M.N. Price, R.P. Koche, K. Keller, I.L. Dubchak, A.P. Arkin. The MicrobesOnline Website for Comparative Genomics. Genome Research, 2005, Jul; 15(7):1015-22
• M.N. Price, E.J. Alm, A.P. Arkin. Interruptions in Gene Expression Drive Highly Expressed Operons to The Leading Strand of DNA Replication. Nucleic Acids Research 2005, 33:3224-34.
• M.N. Price, K.H. Huang, A.P. Arkin, E.J. Alm. Operon Formation is Driven by Co-Regulation and Not by Horizontal Gene Transfer. Genome Research 2005. 15(6):80-19
• Y. Liu et al. Transcriptome Analysis of Shewanella oneidensis MR-1 in Response to Elevated Salt Conditions. J Bacteriol. 2005, 187(7):2501-2507
• M.N. Price, K.H. Huang, E.J. Alm, A.P Arkin. A Novel Method for Accurate Operon Predictions in All Sequenced Prokaryotes Nucleic Acids Research 2005. 33(3):880-892
• D.A. Rodionov, I. Dubchak, A. Arkin, E. Alm, M.S. Gelfand. Reconstruction of Regulatory And Metabolic Pathways in Metal-reducing Delta-proteobacteria. Genome Biology 2004, 5:R90
• H. Gao et al. Global Transcriptome Analysis of the Heat Shock Response of Shewanella oneidensis. J Bacteriol. 2004 Nov;186(22):7796-803.