Publications

1. Davis, J. J., Wattam, A. R., Aziz, R. K., Brettin, T., Butler, R. M., Butler, R., Chlenski, P., Conrad, N., Dickerman, A., Dietrich, E. M., Gabbard, J. L., Gerdes, S., Guard, A., Kenyon, R. W., Machi, D., Mao, C., Murphy-Olson, D., Nguyen, M., Nordberg, E. K., Olsen, G. J., Olson, R. D., Overbeek, J. C., Overbeek, R., Parrello, B., Pusch, G. D., Shukla, M., Thomas, C., VanOeffelen, M., Vonstein, V., Warren, A. S., Xia, F., Xie, D., Yoo, H., and Stevens, R. 2020. The PATRIC bioinformatics resource center: Expanding data and analysis capabilities. Nucleic Acids Res. 48: D606–D612. (doi: 10.1093/nar/gkz943; PubMed: 31667520; PubMed Central: PMC7145515; Academic.oup.com)
2. Zhang, C., Phillips, A. P. R., Wipfler, R. L., Olsen, G. J., and Whitaker, R. J. 2018. The essential genome of the crenarchaeal model Sulfolobus islandicus. Nat. Commun. 9: 4908. (doi: 10.1038/s41467-018-07379-4; PubMed: 30464174; PubMed Central: PMC6249222; Nature.com)
3. Arkin, A. P., Cottingham, R. W., Henry, C. S., Harris, N. L., Stevens, R. L., Maslov, S., Dehal, P., Ware, D., Perez, F., Canon, S., Sneddon, M. W., Henderson, M. L., Riehl, W. J., Murphy-Olson, D., Chan, S., Kamimura, R. T., Kumari, S., Drake, M. M., Brettin, T. S., Glass, E. M., Chivian, D., Gunter, D., Weston, D. J., Allen, B. H., Baumohl, J., Best, A. A., Bowen, B., Brenner, S. E., Bun, C. C., Chandonia, J.-M., Chia, J.-M., Colasanti, R., Conrad, N., Davis, J. J., Davison, B. H., DeJongh, M., Devoid, S., Dietrich, E., Dubchak, I., Edirisinghe, J. N., Fang, G., Faria, J. P., Frybarger, P. M., Gerlach, W., Gerstein, M., Gurtowski, J., Haun, H. L., He, F., Jain, R., Joachimiak, M. P., Keegan, K. P., Kondo, S., Kumar, V., Land, M. L., Meyer, F., Mills, M., Novichkov, P., Oh, T., Olsen, G. J., Olson, B., Parrello, B., Pasternak, S., Pearson, E., Poon, S. S., Price, G. A., Ramakrishnan, S., Ranjan, P., Ronald, P. C., Schatz, M. C., Seaver, S. M. D., Shukla, M., Sutormin, R. A., Syed, M. H., Thomason, J., Tintle, N. L., Wang, D., Xia, F., Yoo, H., Yoo, S., and Yu, D. 2018. KBase: The United States Department of Energy systems biology knowledgebase. Nature BioTech. 36: 566–569. (doi: 10.1038/nbt.4163; PubMed: 29979655; Nature.com)
4. Antonopoulos, D. A., Assaf, R., Aziz, R. K., Brettin, T., Bun, C., Conrad, N., Davis, J. J., Dietrich, E. M., Disz, T., Gerdes, S., Kenyon, R. W., Machi, D., Mao, C., Murphy-Olson, D. E., Nordberg, E. K., Olsen, G. J., Olson, R., Overbeek, R., Parrello, B., Pusch, G. D., Santerre, J., Shukla, M., Stevens, R. L., VanOeffelen, M., Vonstein, V., Warren, A. S., Wattam, A. R., Xia, F., and Yoo, H. 2017. PATRIC as a unique resource for studying antimicrobial resistance. Brief. Bioinform. [Epub ahead of print Jul. 31, 2017] (doi: 10.1093/bib/bbx083; PubMed: 28968762; Academic.oup.com)
5. Wattam, A. R., Davis, J. J., Assaf, R., Boisvert, S., Brettin, T., Bun, C., Conrad, N., Dietrich, E. M., Disz, T., Gabbard, J. L., Gerdes, S., Henry, C. S., Kenyon, R. W., Machi, D., Mao, C., Nordberg, E. K., Olsen, G. J., Murphy-Olson, D. E., Olson, R., Overbeek, R., Parrello, B., Pusch, G. D., Shukla, M., Vonstein, V., Warren, A., Xia, F., Yoo, H., and Stevens, R. L. 2016. Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acids Res. 45: D535–D542. [Epub Nov. 29, 2016] (doi: 10.1093/nar/gkw1017; PubMed: 27899627; PubMed Central: PMC4744870; OxfordJournals.org)
6. Davis, J. J., Gerdes, S., Olsen, G. J., Olson, R., Pusch, G. D, Shukla, M., Vonstein, V., Wattam, A. R., and Yoo, H. 2016. PATtyFams: Protein families for the microbial genomes in the PATRIC database. Frontiers Microbiol. 7: 118. [Epub Jan. 22, 2016] (doi: 10.3389/fmicb.2016.00118; PubMed: 26903996; PubMed Central: PMC4744870; FrontiersIn.org)
7. Wetzel, M. E., Olsen, G. J., Chakravartty, V., and Farrand, S. K. 2015. The repABC plasmids with quorum-regulated transfer systems in members of the Rhizobiales divide into two structurally and separately evolving groups. Genome Biol. Evol. 7: 3337–3357. [Epub Nov. 19, 2015] (doi: 10.1093/gbe/evv227; PubMed: 26590210; PubMed Central: PMC4700958; OxfordJournals.org; Supplementary data)
8. Matthews, T. D., Schmieder, R., Silva, G. G. Z., Busch, J., Cassman, N., Dutilh, B. E., Green, D., Matlock, B., Heffernan, B., Olsen, G. J., Hanna, L. F., Schifferli, D. M., Maloy, S., Dinsdale, E. A., and Edwards, R. A. 2015. Genomic comparison of the closely-related Salmonella enterica serovars Enteritidis, Dublin and Gallinarum. PLoS ONE 10: e0126883. (doi: 10.1371/journal.pone.0126883; PubMed: 26039056; PubMed Central: PMC4454671; PLoS.org; Table S1, Table S2, Table S3, Table S4, Table S5, Table S6, Table S7, Table S8, Table S9, Table S10, Table S11, Table S12, Table S13, Table S14)
9. Brettin, T., Davis, J. J., Disz, T., Edwards, R. A., Gerdes, S., Olsen, G. J., Olson, R., Overbeek, R., Parrello, B., Pusch, G. D., Shukla, M., Thomason, J. A, III, Stevens, R., Vonstein, V., Wattam, A. R., and Xia, F. 2015. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci. Rep. 5: 8365. (doi: 10.1038/srep08365; PubMed: 25666585; PubMed Central: PMC4322359; Nature.com)
10. Wetzel, M. E., Kim, K.-S., Miller, M., Olsen, G. J., and Farrand, S. E. 2014. Quorum-dependent mannopine-inducible conjugative transfer of an Agrobacterium opine-catabolic plasmid. J. Bacteriol. 196: 1031–1044. [Epub Dec. 20, 2013] (doi: 10.1128/JB.01365-13; PubMed: 24363349; PubMed Central: PMC3957693; ASM.org; Supplementary data)
11. Overbeek, R., Olson, R., Pusch, G. D., Olsen, G. J., Davis, J. J., Disz, T., Edwards, R. A., Gerdes, S., Parrello, B., Shukla, M., Vonstein, V., Wattam, A. R., Xia, F., and Stevens, R. 2013. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 42: D206–D214. [Epub Nov. 29, 2013] (doi: 10.1093/nar/gkt1226; PubMed: 24293654; PubMed Central: PMC3965101; OxfordJournals.org)
12. Davis, J. J., Olsen, G. J., Overbeek, R. A., Vonstein, V., and Xia, F. 2014. In search of genome annotation consistency: Solid gene clusters and how to use them. 3 Biotech 4: 331–335. [Epub July 9, 2013] (doi: 10.1007/s13205-013-0152-2; Springerlink.com)
13. Davis, J. J., Xia, F., Overbeek, R. A., and Olsen, G. J. 2013. The genomes of the Erysipelotrichia clarify the firmicute origin of the Mollicutes. Int. J. Syst. Evol. Microbiol. 63: 2727–2741. [Epub Apr. 19, 2013] (doi: 10.1371/journal.pone.0048053; PubMed: 23606477; PubMed Central: PMC3749518; SGMJournals.org; Supplementary material)
14. Aziz, R. K., Devoid, S., Disz, T., Edwards, R. A., Henry, C. S., Olsen, G. J., Olson, R., Overbeek, R., Parrello, B., Pusch, G. D., Stevens, R. L., Vonstein, V., and Xia, F. 2012. SEED Servers: High-performance access to the SEED genomes, annotations, and metabolic models. PLoS ONE 7: e48053. [Epub Oct. 24, 2012] (doi: 10.1099/ijs.0.048983-0; PubMed: 23110173; PubMed Central: PMC3480482; PLoS.org)
15. Karberg, K. A., Olsen, G. J., and Davis, J. J. 2011. Similarity of genes horizontally acquired by Escherichia coli and Salmonella enterica is evidence of a supraspecies pangenome. Proc. Natl. Acad. Sci. USA 108: 20154–20159. [Epub Nov. 29, 2011] (doi: 10.1073/pnas.1109451108; PubMed: 22128332; PubMed Central: PMC3250135; PNAS.org; Supporting information)
16. Rivera, A. J., Frank, J. A., Stumpf, R., Salyers, A. A., Wilson, B. A., Olsen, G. J., and Leigh, S. 2011. Differences between the normal vaginal bacterial community of baboons and that of humans. Am. J. Primatol. 73: 119–126. [Epub Sep 17, 2010] (doi: 10.1002/ajp.20851; PubMed: 20853395; Wiley.com; Supporting information)
17. Davis, J. J., and Olsen, G. J. 2011. Characterizing the native codon usages of a genome: An axis projection approach. Mol. Biol. Evol. 28: 211–221. [Epub Aug. 2, 2010] (doi: 10.1093/molbev/msq185; PubMed: 20679093; PubMed Central: PMC3002238; OxfordJournals.org; Supplementary Data; Programs in gzip tar file; Examples in gzip tar file)
18. Chia, N., Cann, I., and Olsen, G. J. 2010. Evolution of DNA replication protein complexes in Eukaryotes and Archaea. PLoS One 5: e10866. (doi: 10.1371/journal.pone.0010866; PubMed: 20532250; PubMed Central: PMC2880001; PLoS.org; Supporting information)
19. Davis, J. J., and Olsen, G. J. 2010. Modal codon usage: Assessing the typical codon usage of a genome. Mol. Biol. Evol. 27: 800–810. [Epub Dec. 17, 2009] (doi: 10.1093/molbev/msp281; PubMed: 20018979; PubMed Central: PMC2839124; OxfordJournals.org; Supplementary Data; Programs in gzip tar file)
20. Zhang, J., and Olsen, G. J. 2009. Messenger RNA processing in Methanocaldococcus (Methanococcus) jannaschii. RNA 15: 1909–1916. [Epub Aug. 28, 2009] (doi: 10.1261/rna.1715209; PubMed: 19717546; PubMed Central: PMC2743043; CSHLP.com)
21. Zhang, J., Li, E., and Olsen, G. J. 2009. Protein-coding gene promoters in Methanocaldococcus (Methanococcus) jannaschii. Nucleic Acids Res. 37: 3588–3601. [Epub Apr. 9, 2009] (doi: 10.1093/nar/gkp213; PubMed: 19359364; PubMed Central: PMC2699501; OxfordJournals.org; Supplementary data)
22. Kim, T. K., Thomas, S. M., Ho, M., Sharma, S., Reich, C. I., Frank, J. A., Yeater, K. M., Biggs, D., Nakamura, N., Stumpf, R., Leigh, S. R., Tapping, R. I., Blanke, S. R., Slauch, J. M., Gaskins, H. R., Weisbaum, J. S., Olsen, G. J., Hoyer, L. L., and Wilson, B. A. 2009. Heterogeneity of vaginal bacterial communities within individuals. J. Clin. Microbiol. 47: 1181–1189. [Epub Jan. 21, 2009] (doi: 10.1128/JCM.00854-08; PubMed: 19158255; PubMed Central: PMC2668325; ASM.org; Supplemental material)
23. Li, E., Reich, C. I., and Olsen, G. J. 2008. A whole-genome approach to identifying protein binding sites: Promoters in Methanocaldococcus (Methanococcus) jannaschii. Nucleic Acids Res. 36: 6948–6958. [Epub Nov. 3, 2008] (doi: 10.1093/nar/gkm499; PubMed: 18981048; PubMed Central: PMC2602779; OxfordJournals.org; Supplementary data)
24. Anderson, I., Rodriguez, J., Susanti, D., Porat, I., Reich, C., Ulrich, L. E., Elkins, J. G., Mavromatis, K., Lykidis, A., Kim, E., Thompson, L. S., Nolan, M., Land, M., Copeland, A., Lapidus, A., Lucas, S., Detter, C., Zhulin, I. B., Olsen, G. J., Whitman, W., Mukhopadhyay, B., Bristow, J., and Kyrpides, N. 2008. Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction. J. Bacteriol. 190: 2957–2965. [Epub Feb. 8, 2008] (doi: 10.1128/JB.01949-07; PubMed: 18263724; PubMed Central: PMC2293246; ASM.org; Supplemental material)
25. Frank, J. A., Reich, C. I., Sharma, S., Weisbaum, J. S., Wilson, B. A., and Olsen, G. J. 2008. Critical evaluation of two commonly-used primers for amplification of bacterial 16S rRNA genes. Appl. Environ. Microbiol. 74: 2461–2470. [Epub Feb. 22, 2008] (doi: 10.1128/AEM.02272-07; PubMed: 18296538; PubMed Central: PMC2293150; ASM.org)
26. Aziz, R., Bartels, D., Best, A., DeJongh, M., Disz, T., Edwards, R., Formsma, K., Gerdes, S., Glass, E., Kubal, M., Meyer, F., Olsen, G. J., Olson, R., Osterman, A., Overbeek, R., McNeil, L., Paarmann, D., Paczian, T., Parrello, B., Pusch, G. D., Reich, C., Stevens, R., Vassieva, O., Vonstein, V., Wilke, A., and Zagnitko, O. 2008. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics 9: 75. (doi: 10.1186/1471-2164-9-75; PubMed: 18261238; PubMed Central: PMC2265698; BioMedCentral.com)
27. Morrison, H. G., McArthur, A. G., Gillin, F. D., Aley, S. B., Adam, R. D., Olsen, G. J., Best, A. A., Cande, W. Z., Chen, F., Cipriano, M. J., Davids, B. J., Dawson, S. C., Reiner, D. S., Elmendorf, H. G., Hehl, A. B., Holder, M. E., Huse, S. M., Kim, U. U., Lasek-Nesselquist, E., Manning, G., Nigam, A., Nixon, J. E. J., Palm, D., Passamaneck, N. E., Prabhu, A., Reich, C. I., Reiner, D. S., Samuelson, J., Svard, S. G., and Sogin, M. L. 2007. Genomic minimalism in the early diverging, intestinal parasite, Giardia lamblia. Science 317: 1921–1926. (doi: 10.1126/science.1143837; PubMed: 17901334; ScienceMag.com; Supporting material)
28. McNeil, L. K., Reich, C., Aziz, R. K., Bartels, D., Cohoon, M., Disz, T., Edwards, R. A., Gerdes, S., Hwang, K., Kubal, M., Margaryan, G. R., Meyer, F., Mihalo, W., Olsen, G. J., Olson, R., Osterman, A., Paarmann, D., Paczian, T., Parrello, B., Pusch, G. D., Rodionov, D. A., Shi, X., Vassieva, O., Vonstein, V., Zagnitko, O., Xia, F., Zinner, J., Overbeek, R., and Stevens, R. 2007. The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res. 35: D347–353. [Epub Dec. 1, 2006] (doi: 10.1093/nar/gkl947; PubMed: 17145713; PubMed Central: PMC1751540; OxfordJournals.org)
29. Qiao, B., Goldberg, T. L., Olsen, G. J., and Weigel, R. M. 2006. A computer simulation analysis of the accuracy of partial genome sequencing and restriction fragment analysis in the reconstruction of phylogenetic relationships. Infect. Genet. Evol. 6: 323–330. [Epub Jan. 6, 2006] (doi:10.1016/j.meegid.2005.10.002; PubMed: 16406823; Elsevier.com; PDF)
30. Overbeek, R., Begley, T., Butler, R. M., Choudhuri, J. V., Chuang, H.-Y., Cohoon, M., de Crécy-Lagard, V., Diaz, N., Disz, T., Edwards, R., Fonstein, M., Frank, E. D., Gerdes, S., Glass, E. M., Goesmann, A., Hanson, A., Iwata-Reuyl, D., Jensen, R., Jamshidi, N., Krause, L., Kubal, M., Larsen, N., Linke, B., McHardy, A. C., Meyer, F., Neuweger, H., Olsen, G., Olson, R., Osterman, A., Portnoy, V., Pusch, G. D., Rodionov, D. A., Rückert, C., Steiner, J., Stevens, R., Thiele, I., Vassieva, O., Ye, Y., Zagnitko, O., and Vonstein, V. 2005. The subsystems approach to genome annotation and its use in the project to annotate 1,000 genomes. Nucleic Acids Res. 33: 5691–5702. (doi: 10.1093/nar/gki866; PubMed: 16214803; PubMed Central: PMC1251668; OxfordJournals.org)
31. Olsen, G. J. 2005. Bacteriology. In World Book Encyclopedia.
32. Olsen, G. J. 2005. Bacteria. In World Book Encyclopedia.
33. Olsen, G. J. 2005. Archaea. In World Book Encyclopedia.
34. Best, A. A., Morrison, H. G., McArthur, A. G., Sogin, M. L., and Olsen, G. J. 2004. Evolution of eukaryotic transcription: Insights from the genome of Giardia lamblia. Genome Res. 14: 1537–1547. (doi: 10.1101/gr.2256604; PubMed: 15289474; PubMed Central: PMC509262; CSHLP.com; Supplemental data)
35. Zhu, W., Reich, C. I., Olsen, G. J., Giometti, C. S., and Yates, J., III. 2004. Shotgun proteomics of Methanococcus jannaschii and insights into methanogenesis. J. Proteome Res. 3: 538–548. (doi: 10.1021/pr034109s; PubMed: 15253435; ACS.org; Supporting information)
36. Lim, H., Eng, J., Yates, J. R., III, Tollaksen, S. L., Giometti, C. S., Holden, J. F., Adams, M. W. W., Reich, C. I., Olsen, G. J., and Hays, L. G. 2003. Identification of 2D-gel proteins: A comparison of MALDI/TOF peptide mass mapping to µ LC-ESI tandem mass spectrometry. J. Am. Soc. Mass Spectrom. 14: 957–970. (doi: 10.1016/S1044-0305(03)00144-2; PubMed: 12954164; PDF)
37. Giometti, C. S., Reich, C., Tollaksen, S., Babnigg, G., Lim, H., Zhu, W., Yates, J., III, and Olsen, G. 2002. Global analysis of a "simple" proteome: Methanococcus jannaschii. J. Chromatog. B, 782: 227–243. (doi: 10.1016/S1570-0232(02)00568-8; PubMed: 12458009)
38. Kurland, C., and Olsen, G. 2002. Genomics. Curr. Opin. Microbiol. 5: 497–498. (doi: https://doi.org/10.1016/S1369-5274(02)00363-6)
39. Edwards, R. A., Olsen, G. J., and Maloy, S. R. 2002. The importance of complete genome sequences. Trends Microbiol. 10: 220–220. [Letter]
40. Edwards, R. A., Olsen, G. J., and Maloy, S. R. 2002. Comparative genomics of closely related Salmonellae. Trends Microbiol. 10: 94–99. (doi: 10.1016/S0966-842X(01)02293-4; PubMed: 11827811; Elsevier.com; PDF)
41. Stewart, C. A., Hart, D., Berry, D. K., Olsen, G. J., Wernert, E., and Fischer, W. 2001. Parallel implementation and performance of fastDNAml — a program for maximum likelihood phylogenetic inference. Proceedings of SC2001, Denver, CO, November 2001. (PDF)
42. McCloskey, J. A., Graham, D. E., Zhou, S., Crain, P. F., Ibba, M., Konisky, J., Söll, D., and Olsen, G. J. 2001. Posttranslational modifications of archaeal tRNAs: Identities and phylogenetic relations of nucleotides from mesophilic and hyperthermophilic Methanococcales. Nucleic Acids Res. 29: 4699–4706. (doi: 10.1093/nar/29.22.4699; PubMed: 11713320; PubMed Central: PMC92529)
43. Giometti, C. S., Reich, C. I., Tollaksen, S., Babnigg, G., Lim, H., Yates, J. R., III, and Olsen, G. J. 2001. Structural modifications of Methanococcus jannaschii flagellin proteins revealed by proteome analysis. Eur. J. Mass Spectrom. 7: 195–205. (doi: 10.1255/ejms.404; PubMed: 11683504; IMPublications.com) [also published in Proteomics 1: 1033–1042.]
44. Olsen, G. J. 2001. Parsimony. In Brenner, S., and Miller, J. H. (eds.), Encyclopedia of Genetics, Academic Press, London.
45. Reich, C. I., McNeil, L. K., Brace, J. L., Brucker, J. K., and Olsen, G. J. 2001. Archaeal RecA homologs: Different response to DNA damaging agents in mesophilic and thermophilic Archaea. Extremophiles 5: 265–275. (doi: 10.1007/s007920100197; PubMed: 11523896; Springerlink.com)
46. Olsen, G. J. 2001. The history of life. Nat. Genet. 28: 197–198. (doi: 10.1038/90014; PubMed: 11431679; Nature.com) [News and Views]
47. Best, A. A., and Olsen, G. J. 2001. Similar subunit architectures between archaeal and eukaryal RNA polymerases. FEMS Microbiol. Lett. 195: 85–90. (doi: 10.1111/j.1574-6968.2001.tb10502.x; PubMed: 11167000; OxfordJournals.org)
48. Maidak, B. L., Cole, J. R., Lilburn, T. G., Parker, C. T., Jr., Saxman, P. R., Farris, R. J., Garrity, G. M., Olsen, G. J., Schmidt, T. M., and Tiedje, J. M. 2001. The RDP-II. Nucleic Acids Res. 29: 173–174. (doi: 10.1093/nar/29.1.173; PubMed: 11125082; PubMed Central: PMC29785; OxfordJournals.org)
49. Bouzat, J. L., McNeil, L. K., Robertson, H. M., Solter, L. F., Nixon, J., Beever, J. E., Gaskins, H. R., Olsen, G., Subramaniam, S., Sogin, M. L., and Lewin, H. A. 2001. Phylogenetic analysis of the alpha proteasome gene family from early diverging eukaryotes. J. Mol. Evol. 51: 532–543. (doi: 10.1007/s002390010117; PubMed: 11116327; Springer.com)
50. McArthur, A. G., Morrison, H. G., Nixon, J. E. J., Passamaneck, N. Q. E., Kim, U., Hinkle, G., Crocker, M. K., Holder, M. E., Farr, R., Reich, C. I., Olsen, G. J., Aley, S. B., Adam, R., Gillin, F. D., and Sogin, M. L. 2000. The Giardia genome project database. FEMS Microbiol. Lett. 189: 271–273. (doi: 10.1111/j.1574-6968.2000.tb09242.x; PubMed: 10930750; OxfordJournals.org)
51. Graham, D. E., Overbeek, R., Olsen, G. J., and Woese, C. R. 2000. An archaeal genomic signature. Proc. Natl. Acad. Sci. USA 97: 3304–3308. (doi: 10.1073/pnas.97.7.3304; PubMed: 10716711; PubMed Central: PMC16234; PNAS.org)
52. Maidak, B. L., Cole, J. R., Lilburn, T. G., Parker, C. T., Jr., Saxman, P. R., Stredwick, J. M., Garrity, G. M., Li, B., Olsen, G. J., Pramanik, S., Schmidt, T. M., and Tiedje, J. M. 2000. The RDP (Ribosomal Database Project) continues. Nucleic Acids Res. 28: 173–174. (doi: 10.1093/nar/28.1.173; PubMed: 10592216; PubMed Central: PMC102428; OxfordJournals.org)
53. Woese, C. R., Olsen, G. J., Ibba, M., and Söll, D. 2000. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol. Mol. Biol. Rev. 64: 202–236. (doi: 10.1128/MMBR.64.1.202-236.2000; PubMed: 10704480; PubMed Central: PMC98992; ASM.org)
54. Olsen, G. J. 1999. What's eating the free lunch? Nature 300: 403, 405. (doi: 10.1038/22643; PubMed: 10440364; Nature.com) [News and Views]
55. Kyrpides, N. C., and Olsen, G. J. 1999. Archaeal and bacterial hyperthermophiles: Horizontal gene exchange or common ancestry? Trends Genet. 15: 298–299. (doi: 10.1016/S0168-9525(99)01811-9; PubMed: 10431189; ScienceDirect.com)
56. Badger, J. H., and Olsen, G. J. 1999. CRITICA: Coding region identification tool invoking comparative analysis. Mol. Biol. Evol. 16: 512–524. (PubMed: 10331277; OxfordJournals.org)
57. Haney, P. J., Badger, J. H., Buldak, G. L., Reich, C. I., Woese, C. R., and Olsen, G. J. 1999. Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. Proc. Natl. Acad. Sci. USA 96: 3578–3583. (doi: 10.1073/pnas.96.7.3578; PubMed: 10097079; PubMed Central: PMC22336; PNAS.org)
58. Maidak, B. L., Cole, J. R., Parker, Jr., C. T., Garrity, G. M., Larsen, N., Li, B., Lilburn, T. G., McCaughey, M. J., Olsen, G. J., Overbeek, R., Pramanik, S., Schmidt, T. M., Tiedje, J. M., and Woese, C. R. 1999. A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res. 27: 171–173. (doi: 10.1093/nar/27.1.171; PubMed: 9847171; PubMed Central: PMC148126; OxfordJournals.org)
59. Olsen, G. J. 1998. Archaea. In World Book Encyclopedia, pp. 593–593.
60. Deckert, G., Warren, P. V., Gaasterland, T., Young, W. G., Lenox, A. L., Graham, D. E., Overbeek, R., Snead, M. A., Keller, M., Aujay, M., Huber, R., Feldman, R., Short, J. M., Olsen, G. J., and Swanson, R. V. 1998. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature 392: 353–358. (doi: 10.1038/32831; PubMed: 9537320; Nature.com)
61. Selkov, E., Maltsev, N., Olsen, G. J., Overbeek, R., and Whitman, W. B. 1997. A reconstruction of the metabolism of Methanococcus jannaschii from sequence data. Gene 197: GC11-GC26. (doi: 10.1016/S0378-1119(97)00307-7; PubMed: 9332394; ScienceDirect.com)
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94. Olsen, G. J. 1991. Systematic underestimation of tree branch lengths by Lake's operator metrics: An effect of position-dependent substitution rates. Mol. Biol. Evol. 8: 592–608.
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99. Holmes, M. L., Olsen, G. J., and Dyall-Smith, M. L. 1990. The halophilic archaebacteria Hb. lactoprofundi and Hb. saccharovorum are closely related: 16S rRNA sequence comparison. Nucleic Acids Res. 18: 4607–4607. (PubMed: 1697068; PubMed Central: PMC331299)
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107. Turner, S., DeLong, E. F., Giovannoni, S. J., Olsen, G. J., and Pace, N. R. 1989. Phylogenetic analysis of microorganisms and natural populations using rRNA sequences. In Cohen, Y., and Rosenberg, E. (eds.), Microbial Mats: Physiological Ecology of Benthic Microbial Communities, American Society Microbiology, Washington, DC, pp. 390–401.
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118. Reich, C., Olsen, G. J., Pace, B., and Pace, N. R. 1988. Role of the protein moiety of ribonuclease P, a ribonucleoprotein enzyme. Science 239: 178–181. (PubMed: 3122322)
119. Pace, N. R., James, B. D., Reich, C., Waugh, D. S., Olsen, G. J., and Marsh, T. L. 1987. Bacillus subtilis RNase P. In Inouye, M., and Dudock, B. S. (eds.), Molecular Biology of RNA: New perspectives, Academic Press, Orlando, pp. 17–36.
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122. Romaniuk, P. J., Zoltowska, B., Trust, T. J., Lane, D. J., Olsen, G. J., Pace, N. R., and Stahl, D. A. 1987. Campylobacter pylori, the spiral bacterium associated with human gastritis, is not a true Campylobacter sp. J. Bacteriol. 169: 2137–2141. (PubMed: 3571163; PubMed Central: PMC212113)
123. Stahl, D. A., Lane, D. J., Olsen, G. J., Heller, D. J., Schmidt, T. M., and Pace, N. R. 1987. A phylogenetic analysis of certain sulfur-oxidizing and related morphologically conspicuous bacteria by 5S ribosomal RNA sequences. Internat. J. Syst. Bacteriol. 37: 116–122.
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134. Elwood, H. J., Olsen, G. J., and Sogin, M. L. 1985. The small-subunit ribosomal RNA gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata. Mol. Biol. Evol. 2: 399–410. (PubMed: 3939705)
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136. Stahl, D. A., Lane, D. J., Olsen, G. J., and Pace, N. R. 1985. Characterization of a Yellowstone hot spring microbial community by 5S ribosomal RNA sequences. Appl. Environ. Microbiol. 49: 1379–1384. (PubMed: 2409920; PubMed Central: PMC241732)
137. Yang, D., Oyaizu, Y., Oyaizu, H., Olsen, G. J., and Woese, C. R. 1985. Mitochondrial origins. Proc. Natl. Acad. Sci. USA 82: 4443–4447. (PubMed: 3892535; PubMed Central: PMC391117)
138. Rogers, M. J., Simmons, J., Walker, R. T., Weisburg, W. G., Woese, C. R., Tanner, R. S., Robinson, I. M., Stahl, D. A., Olsen, G., Leach, R. H., and Maniloff, J. 1985. Construction of the mycoplasma evolutionary tree from 5S rRNA sequence data. Proc. Natl. Acad. Sci. USA 82: 1160–1164. (PubMed: 2579388; PubMed Central: PMC397214)
139. Pace, N. R., Stahl, D. A., Lane, D. J., and Olsen, G. J. 1985. Analyzing natural microbial populations by rRNA sequences. ASM News 51: 4–12.
140. Seilhamer, J. J., Olsen, G. J., and Cummings, D. J. 1984. Paramecium mitochondrial genes: I. Small subunit rRNA gene sequence and microevolution. J. Biol. Chem. 259: 5167–5172. (PubMed: 6371000)
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142. Olsen, G. J. 1983. Comparative Analysis of Nucleotide Sequence Data. Ph.D. Dissertation, University of Colorado, Health Science Center, Denver, CO.
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145. Walker, T. A., Johnson, K. D., Olsen, G. J., Peters, M. A., and Pace, N. R. 1982. Enzymatic and chemical structure mapping of mouse 28S ribosomal ribonucleic acid contacts in 5.8S ribosomal ribonucleic acid. Biochemistry 21: 2320–2329. (PubMed: 7093191)
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147. Sogin, M. L., and Olsen, G. J. 1980. Identification and mapping of a 60 bp EcoRI fragment in the Dictyostelium discoideum ribosomal DNA. Gene 8: 231–238. (PubMed: 6244213)