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Results: 1 to 20 of 90

1.

Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences.

Utturkar SM, Klingeman DM, Land ML, Schadt CW, Doktycz MJ, Pelletier DA, Brown SD.

Bioinformatics. 2014 Jun 14. pii: btu391. [Epub ahead of print]

PMID:
24930142
[PubMed - as supplied by publisher]
Free Article
2.

Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia.

Brown SD, Nagaraju S, Utturkar S, De Tissera S, Segovia S, Mitchell W, Land ML, Dassanayake A, Köpke M.

Biotechnol Biofuels. 2014 Mar 21;7:40. doi: 10.1186/1754-6834-7-40. eCollection 2014.

PMID:
24655715
[PubMed]
Free PMC Article
3.

Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass.

Wilson CM, Rodriguez M Jr, Johnson CM, Martin SL, Chu TM, Wolfinger RD, Hauser LJ, Land ML, Klingeman DM, Syed MH, Ragauskas AJ, Tschaplinski TJ, Mielenz JR, Brown SD.

Biotechnol Biofuels. 2013 Dec 2;6(1):179. doi: 10.1186/1754-6834-6-179.

PMID:
24295562
[PubMed]
Free PMC Article
4.

Complete Genome Sequence of Micromonospora Strain L5, a Potential Plant-Growth-Regulating Actinomycete, Originally Isolated from Casuarina equisetifolia Root Nodules.

Hirsch AM, Alvarado J, Bruce D, Chertkov O, De Hoff PL, Detter JC, Fujishige NA, Goodwin LA, Han J, Han S, Ivanova N, Land ML, Lum MR, Milani-Nejad N, Nolan M, Pati A, Pitluck S, Tran SS, Woyke T, Valdés M.

Genome Announc. 2013 Sep 26;1(5). pii: e00759-13. doi: 10.1128/genomeA.00759-13.

PMID:
24072863
[PubMed]
Free PMC Article
5.

Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations.

Bollmann A, Sedlacek CJ, Norton J, Laanbroek HJ, Suwa Y, Stein LY, Klotz MG, Arp D, Sayavedra-Soto L, Lu M, Bruce D, Detter C, Tapia R, Han J, Woyke T, Lucas SM, Pitluck S, Pennacchio L, Nolan M, Land ML, Huntemann M, Deshpande S, Han C, Chen A, Kyrpides N, Mavromatis K, Markowitz V, Szeto E, Ivanova N, Mikhailova N, Pagani I, Pati A, Peters L, Ovchinnikova G, Goodwin LA.

Stand Genomic Sci. 2013 Feb 25;7(3):469-82. doi: 10.4056/sigs.3517166. eCollection 2013.

PMID:
24019993
[PubMed]
Free PMC Article
6.

Complete genome sequence of Halorhodospira halophila SL1.

Challacombe JF, Majid S, Deole R, Brettin TS, Bruce D, Delano SF, Detter JC, Gleasner CD, Han CS, Misra M, Reitenga KG, Mikhailova N, Woyke T, Pitluck S, Nolan M, Land ML, Saunders E, Tapia R, Lapidus A, Ivanova N, Hoff WD.

Stand Genomic Sci. 2013 Apr 15;8(2):206-14. doi: 10.4056/sigs.3677284. eCollection 2013.

PMID:
23991253
[PubMed]
Free PMC Article
7.

Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601(T.).

Oosterkamp MJ, Veuskens T, Talarico Saia F, Weelink SA, Goodwin LA, Daligault HE, Bruce DC, Detter JC, Tapia R, Han CS, Land ML, Hauser LJ, Langenhoff AA, Gerritse J, van Berkel WJ, Pieper DH, Junca H, Smidt H, Schraa G, Davids M, Schaap PJ, Plugge CM, Stams AJ.

PLoS One. 2013 Jun 25;8(6):e66971. doi: 10.1371/journal.pone.0066971. Print 2013.

PMID:
23825601
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Genome Sequence of the Obligate Gammaproteobacterial Methanotroph Methylomicrobium album Strain BG8.

Kits KD, Kalyuzhnaya MG, Klotz MG, Jetten MS, Op den Camp HJ, Vuilleumier S, Bringel F, Dispirito AA, Murrell JC, Bruce D, Cheng JF, Copeland A, Goodwin L, Hauser L, Lajus A, Land ML, Lapidus A, Lucas S, Médigue C, Pitluck S, Woyke T, Zeytun A, Stein LY.

Genome Announc. 2013 Apr 11;1(2):e0017013. doi: 10.1128/genomeA.00170-13.

PMID:
23580712
[PubMed]
Free PMC Article
9.

Complete Genome Sequence of the Hyperthermophilic Sulfate-Reducing Bacterium Thermodesulfobacterium geofontis OPF15T.

Elkins JG, Hamilton-Brehm SD, Lucas S, Han J, Lapidus A, Cheng JF, Goodwin LA, Pitluck S, Peters L, Mikhailova N, Davenport KW, Detter JC, Han CS, Tapia R, Land ML, Hauser L, Kyrpides NC, Ivanova NN, Pagani I, Bruce D, Woyke T, Cottingham RW.

Genome Announc. 2013 Apr 11;1(2):e0016213. doi: 10.1128/genomeA.00162-13.

PMID:
23580711
[PubMed]
Free PMC Article
10.

Draft genome sequence of Frankia sp. strain QA3, a nitrogen-fixing actinobacterium isolated from the root nodule of Alnus nitida.

Sen A, Beauchemin N, Bruce D, Chain P, Chen A, Walston Davenport K, Deshpande S, Detter C, Furnholm T, Ghodbhane-Gtari F, Goodwin L, Gtari M, Han C, Han J, Huntemann M, Ivanova N, Kyrpides N, Land ML, Markowitz V, Mavrommatis K, Nolan M, Nouioui I, Pagani I, Pati A, Pitluck S, Santos CL, Sur S, Szeto E, Tavares F, Teshima H, Thakur S, Wall L, Woyke T, Wishart J, Tisa LS.

Genome Announc. 2013 Mar 21;1(2):e0010313. doi: 10.1128/genomeA.00103-13.

PMID:
23516220
[PubMed]
Free PMC Article
11.

Draft genome sequence of Frankia sp. strain CN3, an atypical, noninfective (Nod-) ineffective (Fix-) isolate from Coriaria nepalensis.

Ghodhbane-Gtari F, Beauchemin N, Bruce D, Chain P, Chen A, Walston Davenport K, Deshpande S, Detter C, Furnholm T, Goodwin L, Gtari M, Han C, Han J, Huntemann M, Ivanova N, Kyrpides N, Land ML, Markowitz V, Mavrommatis K, Nolan M, Nouioui I, Pagani I, Pati A, Pitluck S, Santos CL, Sen A, Sur S, Szeto E, Tavares F, Teshima H, Thakur S, Wall L, Woyke T, Tisa LS.

Genome Announc. 2013 Mar 14;1(2):e0008513. doi: 10.1128/genomeA.00085-13.

PMID:
23516212
[PubMed]
Free PMC Article
12.

Complete genome sequence of Marinomonas posidonica type strain (IVIA-Po-181(T)).

Lucas-Elío P, Goodwin L, Woyke T, Pitluck S, Nolan M, Kyrpides NC, Detter JC, Copeland A, Lu M, Bruce D, Detter C, Tapia R, Han S, Land ML, Ivanova N, Mikhailova N, Johnston AW, Sanchez-Amat A.

Stand Genomic Sci. 2012 Oct 10;7(1):31-43. doi: 10.4056/sigs.2976373. Epub 2012 Sep 27.

PMID:
23458837
[PubMed]
Free PMC Article
13.

Complete genome sequence of Thermovibrio ammonificans HB-1(T), a thermophilic, chemolithoautotrophic bacterium isolated from a deep-sea hydrothermal vent.

Giovannelli D, Ricci J, Pérez-Rodríguez I, Hügler M, O'Brien C, Keddis R, Grosche A, Goodwin L, Bruce D, Davenport KW, Detter C, Han J, Han S, Ivanova N, Land ML, Mikhailova N, Nolan M, Pitluck S, Tapia R, Woyke T, Vetriani C.

Stand Genomic Sci. 2012 Oct 10;7(1):82-90. doi: 10.4056/sigs.2856770. Epub 2012 Sep 26.

PMID:
23449845
[PubMed]
Free PMC Article
14.

The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation.

Mavromatis K, Land ML, Brettin TS, Quest DJ, Copeland A, Clum A, Goodwin L, Woyke T, Lapidus A, Klenk HP, Cottingham RW, Kyrpides NC.

PLoS One. 2012;7(12):e48837. doi: 10.1371/journal.pone.0048837. Epub 2012 Dec 12.

PMID:
23251337
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features.

Aklujkar M, Haveman SA, DiDonato R Jr, Chertkov O, Han CS, Land ML, Brown P, Lovley DR.

BMC Genomics. 2012 Dec 10;13:690. doi: 10.1186/1471-2164-13-690.

PMID:
23227809
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Complete genome sequences of Desulfosporosinus orientis DSM765T, Desulfosporosinus youngiae DSM17734T, Desulfosporosinus meridiei DSM13257T, and Desulfosporosinus acidiphilus DSM22704T.

Pester M, Brambilla E, Alazard D, Rattei T, Weinmaier T, Han J, Lucas S, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Peters L, Ovchinnikova G, Teshima H, Detter JC, Han CS, Tapia R, Land ML, Hauser L, Kyrpides NC, Ivanova NN, Pagani I, Huntmann M, Wei CL, Davenport KW, Daligault H, Chain PS, Chen A, Mavromatis K, Markowitz V, Szeto E, Mikhailova N, Pati A, Wagner M, Woyke T, Ollivier B, Klenk HP, Spring S, Loy A.

J Bacteriol. 2012 Nov;194(22):6300-1. doi: 10.1128/JB.01392-12.

PMID:
23105050
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Twenty-one genome sequences from Pseudomonas species and 19 genome sequences from diverse bacteria isolated from the rhizosphere and endosphere of Populus deltoides.

Brown SD, Utturkar SM, Klingeman DM, Johnson CM, Martin SL, Land ML, Lu TY, Schadt CW, Doktycz MJ, Pelletier DA.

J Bacteriol. 2012 Nov;194(21):5991-3. doi: 10.1128/JB.01243-12.

PMID:
23045501
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Complete genome sequence of Desulfurococcus fermentans, a hyperthermophilic cellulolytic crenarchaeon isolated from a freshwater hot spring in Kamchatka, Russia.

Susanti D, Johnson EF, Rodriguez JR, Anderson I, Perevalova AA, Kyrpides N, Lucas S, Han J, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Mavrommatis K, Peters L, Land ML, Hauser L, Gopalan V, Chan PP, Lowe TM, Atomi H, Bonch-Osmolovskaya EA, Woyke T, Mukhopadhyay B.

J Bacteriol. 2012 Oct;194(20):5703-4.

PMID:
23012283
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Draft genome sequences for two metal-reducing Pelosinus fermentans strains isolated from a Cr(VI)-contaminated site and for type strain R7.

Brown SD, Podar M, Klingeman DM, Johnson CM, Yang ZK, Utturkar SM, Land ML, Mosher JJ, Hurt RA Jr, Phelps TJ, Palumbo AV, Arkin AP, Hazen TC, Elias DA.

J Bacteriol. 2012 Sep;194(18):5147-8. doi: 10.1128/JB.01174-12.

PMID:
22933770
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Complete genome sequences of six strains of the genus Methylobacterium.

Marx CJ, Bringel F, Chistoserdova L, Moulin L, Farhan Ul Haque M, Fleischman DE, Gruffaz C, Jourand P, Knief C, Lee MC, Muller EE, Nadalig T, Peyraud R, Roselli S, Russ L, Goodwin LA, Ivanova N, Kyrpides N, Lajus A, Land ML, Médigue C, Mikhailova N, Nolan M, Woyke T, Stolyar S, Vorholt JA, Vuilleumier S.

J Bacteriol. 2012 Sep;194(17):4746-8. doi: 10.1128/JB.01009-12.

PMID:
22887658
[PubMed - indexed for MEDLINE]
Free PMC Article

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