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FastTree 2--approximately maximum-likelihood trees for large alignments.
Price MN, Dehal PS, Arkin AP. Price MN, et al. PLoS One. 2010 Mar 10;5(3):e9490. doi: 10.1371/journal.pone.0009490. PLoS One. 2010. PMID: 20224823 Free PMC article.
The MicrobesOnline Web site for comparative genomics.
Alm EJ, Huang KH, Price MN, Koche RP, Keller K, Dubchak IL, Arkin AP. Alm EJ, et al. Genome Res. 2005 Jul;15(7):1015-22. doi: 10.1101/gr.3844805. Genome Res. 2005. PMID: 15998914 Free PMC article.
FastBLAST: homology relationships for millions of proteins.
Price MN, Dehal PS, Arkin AP. Price MN, et al. PLoS One. 2008;3(10):e3589. doi: 10.1371/journal.pone.0003589. Epub 2008 Oct 31. PLoS One. 2008. PMID: 18974889 Free PMC article.
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. Dehal PS, et al. Nucleic Acids Res. 2010 Jan;38(Database issue):D396-400. doi: 10.1093/nar/gkp919. Epub 2009 Nov 11. Nucleic Acids Res. 2010. PMID: 19906701 Free PMC article.
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. Chhabra SR, et al. PLoS One. 2011;6(6):e21470. doi: 10.1371/journal.pone.0021470. Epub 2011 Jun 28. PLoS One. 2011. PMID: 21738675 Free PMC article.
A Comparison of the Costs and Benefits of Bacterial Gene Expression.
Price MN, Wetmore KM, Deutschbauer AM, Arkin AP. Price MN, et al. PLoS One. 2016 Oct 6;11(10):e0164314. doi: 10.1371/journal.pone.0164314. eCollection 2016. PLoS One. 2016. PMID: 27711251 Free PMC article.
Validating regulatory predictions from diverse bacteria with mutant fitness data.
Sagawa S, Price MN, Deutschbauer AM, Arkin AP. Sagawa S, et al. PLoS One. 2017 May 24;12(5):e0178258. doi: 10.1371/journal.pone.0178258. eCollection 2017. PLoS One. 2017. PMID: 28542589 Free PMC article.
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