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Items: 31

1.

Transfer RNAs with novel cloverleaf structures.

Mukai T, Vargas-Rodriguez O, Englert M, Tripp HJ, Ivanova NN, Rubin EM, Kyrpides NC, Söll D.

Nucleic Acids Res. 2017 Mar 17;45(5):2776-2785. doi: 10.1093/nar/gkw898.

2.

[Facile Recoding of Selenocysteine in Nature].

Mukai T, Englert M, Tripp HJ, Miller C, Ivanova NN, Rubin EM, Kyrpides NC, Söll D.

Angew Chem Weinheim Bergstr Ger. 2016 Apr 18;128(17):5423-5427. Epub 2016 Mar 15. German. No abstract available.

3.

Erratum to: The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4).

Huntemann M, Ivanova NN, Mavromatis K, Tripp HJ, Paez-Espino D, Palaniappan K, Szeto E, Pillay M, Chen IM, Pati A, Nielsen T, Markowitz VM, Kyrpides NC.

Stand Genomic Sci. 2016 Mar 21;11:27. doi: 10.1186/s40793-016-0148-8. eCollection 2016.

4.

Facile Recoding of Selenocysteine in Nature.

Mukai T, Englert M, Tripp HJ, Miller C, Ivanova NN, Rubin EM, Kyrpides NC, Söll D.

Angew Chem Int Ed Engl. 2016 Apr 18;55(17):5337-41. doi: 10.1002/anie.201511657. Epub 2016 Mar 16.

5.

The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4).

Huntemann M, Ivanova NN, Mavromatis K, Tripp HJ, Paez-Espino D, Tennessen K, Palaniappan K, Szeto E, Pillay M, Chen IM, Pati A, Nielsen T, Markowitz VM, Kyrpides NC.

Stand Genomic Sci. 2016 Feb 24;11:17. doi: 10.1186/s40793-016-0138-x. eCollection 2016.

6.

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4).

Huntemann M, Ivanova NN, Mavromatis K, Tripp HJ, Paez-Espino D, Palaniappan K, Szeto E, Pillay M, Chen IM, Pati A, Nielsen T, Markowitz VM, Kyrpides NC.

Stand Genomic Sci. 2015 Oct 26;10:86. doi: 10.1186/s40793-015-0077-y. eCollection 2015. Erratum in: Stand Genomic Sci. 2016;11:27.

7.

Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology.

Oulas A, Polymenakou PN, Seshadri R, Tripp HJ, Mandalakis M, Paez-Espino AD, Pati A, Chain P, Nomikou P, Carey S, Kilias S, Christakis C, Kotoulas G, Magoulas A, Ivanova NN, Kyrpides NC.

Environ Microbiol. 2016 Apr;18(4):1122-36. doi: 10.1111/1462-2920.13095. Epub 2015 Dec 21.

8.

Toward a standard in structural genome annotation for prokaryotes.

Tripp HJ, Sutton G, White O, Wortman J, Pati A, Mikhailova N, Ovchinnikova G, Payne SH, Kyrpides NC, Ivanova N.

Stand Genomic Sci. 2015 Jul 25;10:45. doi: 10.1186/s40793-015-0034-9. eCollection 2015.

9.

Comparative transcriptomics between Synechococcus PCC 7942 and Synechocystis PCC 6803 provide insights into mechanisms of stress acclimation.

Billis K, Billini M, Tripp HJ, Kyrpides NC, Mavromatis K.

PLoS One. 2014 Oct 23;9(10):e109738. doi: 10.1371/journal.pone.0109738. eCollection 2014.

10.

nifH pyrosequencing reveals the potential for location-specific soil chemistry to influence N2 -fixing community dynamics.

Collavino MM, Tripp HJ, Frank IE, Vidoz ML, Calderoli PA, Donato M, Zehr JP, Aguilar OM.

Environ Microbiol. 2014 Oct;16(10):3211-23. doi: 10.1111/1462-2920.12423. Epub 2014 Mar 19.

11.

ARBitrator: a software pipeline for on-demand retrieval of auto-curated nifH sequences from GenBank.

Heller P, Tripp HJ, Turk-Kubo K, Zehr JP.

Bioinformatics. 2014 Oct 15;30(20):2883-90. doi: 10.1093/bioinformatics/btu417. Epub 2014 Jul 2.

PMID:
24990605
12.

Stop codon reassignments in the wild.

Ivanova NN, Schwientek P, Tripp HJ, Rinke C, Pati A, Huntemann M, Visel A, Woyke T, Kyrpides NC, Rubin EM.

Science. 2014 May 23;344(6186):909-13. doi: 10.1126/science.1250691.

13.

The unique metabolism of SAR11 aquatic bacteria.

Tripp HJ.

J Microbiol. 2013 Apr;51(2):147-53. doi: 10.1007/s12275-013-2671-2. Epub 2013 Apr 27. Review.

PMID:
23625213
14.

Genomic deletions disrupt nitrogen metabolism pathways of a cyanobacterial diatom symbiont.

Hilton JA, Foster RA, Tripp HJ, Carter BJ, Zehr JP, Villareal TA.

Nat Commun. 2013;4:1767. doi: 10.1038/ncomms2748.

15.

Two Strains of Crocosphaera watsonii with Highly Conserved Genomes are Distinguished by Strain-Specific Features.

Bench SR, Ilikchyan IN, Tripp HJ, Zehr JP.

Front Microbiol. 2011 Dec 29;2:261. doi: 10.3389/fmicb.2011.00261. eCollection 2011.

16.

Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies.

Tripp HJ, Hewson I, Boyarsky S, Stuart JM, Zehr JP.

Nucleic Acids Res. 2011 Nov 1;39(20):8792-802. doi: 10.1093/nar/gkr576. Epub 2011 Jul 19.

17.

Unicellular cyanobacteria with a new mode of life: the lack of photosynthetic oxygen evolution allows nitrogen fixation to proceed.

Bothe H, Tripp HJ, Zehr JP.

Arch Microbiol. 2010 Oct;192(10):783-90. doi: 10.1007/s00203-010-0621-5. Epub 2010 Aug 29. Review.

PMID:
20803290
18.

Spatial patterns and light-driven variation of microbial population gene expression in surface waters of the oligotrophic open ocean.

Hewson I, Poretsky RS, Tripp HJ, Montoya JP, Zehr JP.

Environ Microbiol. 2010 Jul;12(7):1940-56. doi: 10.1111/j.1462-2920.2010.02198.x. Epub 2010 Apr 14.

PMID:
20406287
19.

Metabolic streamlining in an open-ocean nitrogen-fixing cyanobacterium.

Tripp HJ, Bench SR, Turk KA, Foster RA, Desany BA, Niazi F, Affourtit JP, Zehr JP.

Nature. 2010 Mar 4;464(7285):90-4. doi: 10.1038/nature08786. Epub 2010 Feb 21.

PMID:
20173737
20.

The presence of the glycolysis operon in SAR11 genomes is positively correlated with ocean productivity.

Schwalbach MS, Tripp HJ, Steindler L, Smith DP, Giovannoni SJ.

Environ Microbiol. 2010 Feb;12(2):490-500. doi: 10.1111/j.1462-2920.2009.02092.x. Epub 2009 Nov 3.

PMID:
19889000
21.

Microbial community gene expression within colonies of the diazotroph, Trichodesmium, from the Southwest Pacific Ocean.

Hewson I, Poretsky RS, Dyhrman ST, Zielinski B, White AE, Tripp HJ, Montoya JP, Zehr JP.

ISME J. 2009 Nov;3(11):1286-300. doi: 10.1038/ismej.2009.75. Epub 2009 Jul 2.

PMID:
19571897
22.

In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii.

Hewson I, Poretsky RS, Beinart RA, White AE, Shi T, Bench SR, Moisander PH, Paerl RW, Tripp HJ, Montoya JP, Moran MA, Zehr JP.

ISME J. 2009 May;3(5):618-31. doi: 10.1038/ismej.2009.8. Epub 2009 Feb 19.

PMID:
19225552
23.

Unique glycine-activated riboswitch linked to glycine-serine auxotrophy in SAR11.

Tripp HJ, Schwalbach MS, Meyer MM, Kitner JB, Breaker RR, Giovannoni SJ.

Environ Microbiol. 2009 Jan;11(1):230-8. doi: 10.1111/j.1462-2920.2008.01758.x.

24.

Globally distributed uncultivated oceanic N2-fixing cyanobacteria lack oxygenic photosystem II.

Zehr JP, Bench SR, Carter BJ, Hewson I, Niazi F, Shi T, Tripp HJ, Affourtit JP.

Science. 2008 Nov 14;322(5904):1110-2. doi: 10.1126/science.1165340.

25.

The small genome of an abundant coastal ocean methylotroph.

Giovannoni SJ, Hayakawa DH, Tripp HJ, Stingl U, Givan SA, Cho JC, Oh HM, Kitner JB, Vergin KL, Rappé MS.

Environ Microbiol. 2008 Jul;10(7):1771-82. doi: 10.1111/j.1462-2920.2008.01598.x. Epub 2008 Apr 3.

PMID:
18393994
26.

SAR11 marine bacteria require exogenous reduced sulphur for growth.

Tripp HJ, Kitner JB, Schwalbach MS, Dacey JW, Wilhelm LJ, Giovannoni SJ.

Nature. 2008 Apr 10;452(7188):741-4. doi: 10.1038/nature06776. Epub 2008 Mar 12.

PMID:
18337719
28.

Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data.

Wilhelm LJ, Tripp HJ, Givan SA, Smith DP, Giovannoni SJ.

Biol Direct. 2007 Nov 7;2:27.

29.

High intraspecific recombination rate in a native population of Candidatus pelagibacter ubique (SAR11).

Vergin KL, Tripp HJ, Wilhelm LJ, Denver DR, Rappé MS, Giovannoni SJ.

Environ Microbiol. 2007 Oct;9(10):2430-40.

PMID:
17803769
30.

Proteorhodopsin in the ubiquitous marine bacterium SAR11.

Giovannoni SJ, Bibbs L, Cho JC, Stapels MD, Desiderio R, Vergin KL, Rappé MS, Laney S, Wilhelm LJ, Tripp HJ, Mathur EJ, Barofsky DF.

Nature. 2005 Nov 3;438(7064):82-5.

PMID:
16267553
31.

Genome streamlining in a cosmopolitan oceanic bacterium.

Giovannoni SJ, Tripp HJ, Givan S, Podar M, Vergin KL, Baptista D, Bibbs L, Eads J, Richardson TH, Noordewier M, Rappé MS, Short JM, Carrington JC, Mathur EJ.

Science. 2005 Aug 19;309(5738):1242-5.

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