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Items: 1 to 50 of 109

1.

The essential genome of the crenarchaeal model Sulfolobus islandicus.

Zhang C, Phillips APR, Wipfler RL, Olsen GJ, Whitaker RJ.

Nat Commun. 2018 Nov 21;9(1):4908. doi: 10.1038/s41467-018-07379-4.

2.

KBase: The United States Department of Energy Systems Biology Knowledgebase.

Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, Kamimura RT, Kumari S, Drake MM, Brettin TS, Glass EM, Chivian D, Gunter D, Weston DJ, Allen BH, Baumohl J, Best AA, Bowen B, Brenner SE, Bun CC, Chandonia JM, Chia JM, Colasanti R, Conrad N, Davis JJ, Davison BH, DeJongh M, Devoid S, Dietrich E, Dubchak I, Edirisinghe JN, Fang G, Faria JP, Frybarger PM, Gerlach W, Gerstein M, Greiner A, Gurtowski J, Haun HL, He F, Jain R, Joachimiak MP, Keegan KP, Kondo S, Kumar V, Land ML, Meyer F, Mills M, Novichkov PS, Oh T, Olsen GJ, Olson R, Parrello B, Pasternak S, Pearson E, Poon SS, Price GA, Ramakrishnan S, Ranjan P, Ronald PC, Schatz MC, Seaver SMD, Shukla M, Sutormin RA, Syed MH, Thomason J, Tintle NL, Wang D, Xia F, Yoo H, Yoo S, Yu D.

Nat Biotechnol. 2018 Jul 6;36(7):566-569. doi: 10.1038/nbt.4163. No abstract available.

3.

PATRIC as a unique resource for studying antimicrobial resistance.

Antonopoulos DA, Assaf R, Aziz RK, Brettin T, Bun C, Conrad N, Davis JJ, Dietrich EM, Disz T, Gerdes S, Kenyon RW, Machi D, Mao C, Murphy-Olson DE, Nordberg EK, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Santerre J, Shukla M, Stevens RL, VanOeffelen M, Vonstein V, Warren AS, Wattam AR, Xia F, Yoo H.

Brief Bioinform. 2017 Jul 31. doi: 10.1093/bib/bbx083. [Epub ahead of print]

PMID:
28968762
4.

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center.

Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T, Bun C, Conrad N, Dietrich EM, Disz T, Gabbard JL, Gerdes S, Henry CS, Kenyon RW, Machi D, Mao C, Nordberg EK, Olsen GJ, Murphy-Olson DE, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Vonstein V, Warren A, Xia F, Yoo H, Stevens RL.

Nucleic Acids Res. 2017 Jan 4;45(D1):D535-D542. doi: 10.1093/nar/gkw1017. Epub 2016 Nov 29.

5.

PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database.

Davis JJ, Gerdes S, Olsen GJ, Olson R, Pusch GD, Shukla M, Vonstein V, Wattam AR, Yoo H.

Front Microbiol. 2016 Feb 8;7:118. doi: 10.3389/fmicb.2016.00118. eCollection 2016.

6.

The repABC Plasmids with Quorum-Regulated Transfer Systems in Members of the Rhizobiales Divide into Two Structurally and Separately Evolving Groups.

Wetzel ME, Olsen GJ, Chakravartty V, Farrand SK.

Genome Biol Evol. 2015 Nov 19;7(12):3337-57. doi: 10.1093/gbe/evv227.

7.

Genomic Comparison of the Closely-Related Salmonella enterica Serovars Enteritidis, Dublin and Gallinarum.

Matthews TD, Schmieder R, Silva GG, Busch J, Cassman N, Dutilh BE, Green D, Matlock B, Heffernan B, Olsen GJ, Farris Hanna L, Schifferli DM, Maloy S, Dinsdale EA, Edwards RA.

PLoS One. 2015 Jun 3;10(6):e0126883. doi: 10.1371/journal.pone.0126883. eCollection 2015.

8.

RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes.

Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Thomason JA 3rd, Stevens R, Vonstein V, Wattam AR, Xia F.

Sci Rep. 2015 Feb 10;5:8365. doi: 10.1038/srep08365.

9.

In search of genome annotation consistency: solid gene clusters and how to use them.

Davis JJ, Olsen GJ, Overbeek R, Vonstein V, Xia F.

3 Biotech. 2014 Jun;4(3):331-335. doi: 10.1007/s13205-013-0152-2. Epub 2013 Jul 6.

10.

Quorum-dependent mannopine-inducible conjugative transfer of an Agrobacterium opine-catabolic plasmid.

Wetzel ME, Kim KS, Miller M, Olsen GJ, Farrand SK.

J Bacteriol. 2014 Mar;196(5):1031-44. doi: 10.1128/JB.01365-13. Epub 2013 Dec 20.

11.

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).

Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R.

Nucleic Acids Res. 2014 Jan;42(Database issue):D206-14. doi: 10.1093/nar/gkt1226. Epub 2013 Nov 29.

12.

Genomes of the class Erysipelotrichia clarify the firmicute origin of the class Mollicutes.

Davis JJ, Xia F, Overbeek RA, Olsen GJ.

Int J Syst Evol Microbiol. 2013 Jul;63(Pt 7):2727-41. doi: 10.1099/ijs.0.048983-0. Epub 2013 Apr 19.

13.

SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models.

Aziz RK, Devoid S, Disz T, Edwards RA, Henry CS, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Stevens RL, Vonstein V, Xia F.

PLoS One. 2012;7(10):e48053. doi: 10.1371/journal.pone.0048053. Epub 2012 Oct 24.

14.

Similarity of genes horizontally acquired by Escherichia coli and Salmonella enterica is evidence of a supraspecies pangenome.

Karberg KA, Olsen GJ, Davis JJ.

Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):20154-9. doi: 10.1073/pnas.1109451108. Epub 2011 Nov 29.

15.

Differences between the normal vaginal bacterial community of baboons and that of humans.

Rivera AJ, Frank JA, Stumpf R, Salyers AA, Wilson BA, Olsen GJ, Leigh S.

Am J Primatol. 2011 Feb;73(2):119-26. doi: 10.1002/ajp.20851. Epub 2010 Sep 17.

PMID:
20853395
16.

Characterizing the native codon usages of a genome: an axis projection approach.

Davis JJ, Olsen GJ.

Mol Biol Evol. 2011 Jan;28(1):211-21. doi: 10.1093/molbev/msq185. Epub 2010 Aug 2.

17.

Evolution of DNA replication protein complexes in eukaryotes and Archaea.

Chia N, Cann I, Olsen GJ.

PLoS One. 2010 Jun 2;5(6):e10866. doi: 10.1371/journal.pone.0010866.

18.

Modal codon usage: assessing the typical codon usage of a genome.

Davis JJ, Olsen GJ.

Mol Biol Evol. 2010 Apr;27(4):800-10. doi: 10.1093/molbev/msp281. Epub 2009 Dec 17.

19.

Messenger RNA processing in Methanocaldococcus (Methanococcus) jannaschii.

Zhang J, Olsen GJ.

RNA. 2009 Oct;15(10):1909-16. doi: 10.1261/rna.1715209. Epub 2009 Aug 28.

20.

Protein-coding gene promoters in Methanocaldococcus (Methanococcus) jannaschii.

Zhang J, Li E, Olsen GJ.

Nucleic Acids Res. 2009 Jun;37(11):3588-601. doi: 10.1093/nar/gkp213. Epub 2009 Apr 9.

21.

Heterogeneity of vaginal microbial communities within individuals.

Kim TK, Thomas SM, Ho M, Sharma S, Reich CI, Frank JA, Yeater KM, Biggs DR, Nakamura N, Stumpf R, Leigh SR, Tapping RI, Blanke SR, Slauch JM, Gaskins HR, Weisbaum JS, Olsen GJ, Hoyer LL, Wilson BA.

J Clin Microbiol. 2009 Apr;47(4):1181-9. doi: 10.1128/JCM.00854-08. Epub 2009 Jan 21.

22.

A whole-genome approach to identifying protein binding sites: promoters in Methanocaldococcus (Methanococcus) jannaschii.

Li E, Reich CI, Olsen GJ.

Nucleic Acids Res. 2008 Dec;36(22):6948-58. doi: 10.1093/nar/gkm499. Epub 2008 Nov 3.

23.

Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes.

Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA, Olsen GJ.

Appl Environ Microbiol. 2008 Apr;74(8):2461-70. doi: 10.1128/AEM.02272-07. Epub 2008 Feb 22.

24.

Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction.

Anderson I, Rodriguez J, Susanti D, Porat I, Reich C, Ulrich LE, Elkins JG, Mavromatis K, Lykidis A, Kim E, Thompson LS, Nolan M, Land M, Copeland A, Lapidus A, Lucas S, Detter C, Zhulin IB, Olsen GJ, Whitman W, Mukhopadhyay B, Bristow J, Kyrpides N.

J Bacteriol. 2008 Apr;190(8):2957-65. doi: 10.1128/JB.01949-07. Epub 2008 Feb 8.

25.

The RAST Server: rapid annotations using subsystems technology.

Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O.

BMC Genomics. 2008 Feb 8;9:75. doi: 10.1186/1471-2164-9-75.

26.

Genomic minimalism in the early diverging intestinal parasite Giardia lamblia.

Morrison HG, McArthur AG, Gillin FD, Aley SB, Adam RD, Olsen GJ, Best AA, Cande WZ, Chen F, Cipriano MJ, Davids BJ, Dawson SC, Elmendorf HG, Hehl AB, Holder ME, Huse SM, Kim UU, Lasek-Nesselquist E, Manning G, Nigam A, Nixon JE, Palm D, Passamaneck NE, Prabhu A, Reich CI, Reiner DS, Samuelson J, Svard SG, Sogin ML.

Science. 2007 Sep 28;317(5846):1921-6.

27.

The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation.

McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes S, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman A, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko O, Xia F, Zinner J, Overbeek R, Stevens R.

Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53. Epub 2006 Dec 1.

28.
29.

Evolution of eukaryotic transcription: insights from the genome of Giardia lamblia.

Best AA, Morrison HG, McArthur AG, Sogin ML, Olsen GJ.

Genome Res. 2004 Aug;14(8):1537-47.

30.

Shotgun proteomics of Methanococcus jannaschii and insights into methanogenesis.

Zhu W, Reich CI, Olsen GJ, Giometti CS, Yates JR 3rd.

J Proteome Res. 2004 May-Jun;3(3):538-48.

PMID:
15253435
31.

Identification of 2D-gel proteins: a comparison of MALDI/TOF peptide mass mapping to mu LC-ESI tandem mass spectrometry.

Lim H, Eng J, Yates JR 3rd, Tollaksen SL, Giometti CS, Holden JF, Adams MW, Reich CI, Olsen GJ, Hays LG.

J Am Soc Mass Spectrom. 2003 Sep;14(9):957-70.

32.

Comparative genomics of closely related salmonellae.

Edwards RA, Olsen GJ, Maloy SR.

Trends Microbiol. 2002 Feb;10(2):94-9. Review.

PMID:
11827811
33.

Post-transcriptional modification in archaeal tRNAs: identities and phylogenetic relations of nucleotides from mesophilic and hyperthermophilic Methanococcales.

McCloskey JA, Graham DE, Zhou S, Crain PF, Ibba M, Konisky J, Söll D, Olsen GJ.

Nucleic Acids Res. 2001 Nov 15;29(22):4699-706.

34.

Structural modifications of Methanococcus jannaschii flagellin proteins revealed by proteome analysis.

Giometti CS, Reich CI, Tollaksen SL, Babnigg G, Lim H, Yates JR 3rd, Olsen GJ.

Proteomics. 2001 Aug;1(8):1033-42.

PMID:
11683504
35.

Archaeal RecA homologues: different response to DNA-damaging agents in mesophilic and thermophilic Archaea.

Reich CI, McNeil LK, Brace JL, Brucker JK, Olsen GJ.

Extremophiles. 2001 Aug;5(4):265-75.

PMID:
11523896
36.

The history of life.

Olsen GJ.

Nat Genet. 2001 Jul;28(3):197-8. No abstract available.

PMID:
11431679
37.

Similar subunit architecture of archaeal and eukaryal RNA polymerases.

Best AA, Olsen GJ.

FEMS Microbiol Lett. 2001 Feb 5;195(1):85-90.

38.

The RDP-II (Ribosomal Database Project).

Maidak BL, Cole JR, Lilburn TG, Parker CT Jr, Saxman PR, Farris RJ, Garrity GM, Olsen GJ, Schmidt TM, Tiedje JM.

Nucleic Acids Res. 2001 Jan 1;29(1):173-4.

39.

An archaeal genomic signature.

Graham DE, Overbeek R, Olsen GJ, Woese CR.

Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3304-8.

40.

Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process.

Woese CR, Olsen GJ, Ibba M, Söll D.

Microbiol Mol Biol Rev. 2000 Mar;64(1):202-36. Review.

41.

The RDP (Ribosomal Database Project) continues.

Maidak BL, Cole JR, Lilburn TG, Parker CT Jr, Saxman PR, Stredwick JM, Garrity GM, Li B, Olsen GJ, Pramanik S, Schmidt TM, Tiedje JM.

Nucleic Acids Res. 2000 Jan 1;28(1):173-4.

42.

Microbiology. What's eating the free lunch?

Olsen GJ.

Nature. 1999 Jul 29;400(6743):403, 405. No abstract available.

PMID:
10440364
43.

Archaeal and bacterial hyperthermophiles: horizontal gene exchange or common ancestry?

Kyrpides NC, Olsen GJ.

Trends Genet. 1999 Aug;15(8):298-9. No abstract available.

PMID:
10431189
44.

CRITICA: coding region identification tool invoking comparative analysis.

Badger JH, Olsen GJ.

Mol Biol Evol. 1999 Apr;16(4):512-24.

PMID:
10331277
45.

Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species.

Haney PJ, Badger JH, Buldak GL, Reich CI, Woese CR, Olsen GJ.

Proc Natl Acad Sci U S A. 1999 Mar 30;96(7):3578-83.

46.

A new version of the RDP (Ribosomal Database Project).

Maidak BL, Cole JR, Parker CT Jr, Garrity GM, Larsen N, Li B, Lilburn TG, McCaughey MJ, Olsen GJ, Overbeek R, Pramanik S, Schmidt TM, Tiedje JM, Woese CR.

Nucleic Acids Res. 1999 Jan 1;27(1):171-3.

47.

The complete genome of the hyperthermophilic bacterium Aquifex aeolicus.

Deckert G, Warren PV, Gaasterland T, Young WG, Lenox AL, Graham DE, Overbeek R, Snead MA, Keller M, Aujay M, Huber R, Feldman RA, Short JM, Olsen GJ, Swanson RV.

Nature. 1998 Mar 26;392(6674):353-8.

PMID:
9537320
48.

The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus.

Klenk HP, Clayton RA, Tomb JF, White O, Nelson KE, Ketchum KA, Dodson RJ, Gwinn M, Hickey EK, Peterson JD, Richardson DL, Kerlavage AR, Graham DE, Kyrpides NC, Fleischmann RD, Quackenbush J, Lee NH, Sutton GG, Gill S, Kirkness EF, Dougherty BA, McKenney K, Adams MD, Loftus B, Peterson S, Reich CI, McNeil LK, Badger JH, Glodek A, Zhou L, Overbeek R, Gocayne JD, Weidman JF, McDonald L, Utterback T, Cotton MD, Spriggs T, Artiach P, Kaine BP, Sykes SM, Sadow PW, D'Andrea KP, Bowman C, Fujii C, Garland SA, Mason TM, Olsen GJ, Fraser CM, Smith HO, Woese CR, Venter JC.

Nature. 1997 Nov 27;390(6658):364-70. Erratum in: Nature 1998 Jul 2;394(6688):101.

PMID:
9389475
49.

A reconstruction of the metabolism of Methanococcus jannaschii from sequence data.

Selkov E, Maltsev N, Olsen GJ, Overbeek R, Whitman WB.

Gene. 1997 Sep 15;197(1-2):GC11-26.

PMID:
9332394
50.

Archaeal genomics: an overview.

Olsen GJ, Woese CR.

Cell. 1997 Jun 27;89(7):991-4. Review. No abstract available.

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