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Results: 1 to 20 of 54

1.

Improved performance of the PacBio SMRT technology for 16S rDNA sequencing.

Mosher JJ, Bowman B, Bernberg EL, Shevchenko O, Kan J, Korlach J, Kaplan LA.

J Microbiol Methods. 2014 Jun 27;104C:59-60. doi: 10.1016/j.mimet.2014.06.012. [Epub ahead of print]

PMID:
24978594
[PubMed - as supplied by publisher]
2.

Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences.

Cao B, Chen C, DeMott MS, Cheng Q, Clark TA, Xiong X, Zheng X, Butty V, Levine SS, Yuan G, Boitano M, Luong K, Song Y, Zhou X, Deng Z, Turner SW, Korlach J, You D, Wang L, Chen S, Dedon PC.

Nat Commun. 2014 Jun 5;5:3951. doi: 10.1038/ncomms4951.

PMID:
24899568
[PubMed - in process]
3.

Complete Genome Sequences of Two Escherichia coli O145:H28 Outbreak Strains of Food Origin.

Cooper KK, Mandrell RE, Louie JW, Korlach J, Clark TA, Parker CT, Huynh S, Chain PS, Ahmed S, Carter MQ.

Genome Announc. 2014 May 22;2(3). pii: e00482-14. doi: 10.1128/genomeA.00482-14.

PMID:
24855308
[PubMed]
Free PMC Article
4.

Identification of restriction-modification systems of Bifidobacterium animalis subsp. lactis CNCM I-2494 by SMRT sequencing and associated methylome analysis.

O' Connell Motherway M, Watson D, Bottacini F, Clark TA, Roberts RJ, Korlach J, Garault P, Chervaux C, van Hylckama Vlieg JE, Smokvina T, van Sinderen D.

PLoS One. 2014 Apr 17;9(4):e94875. doi: 10.1371/journal.pone.0094875. eCollection 2014.

PMID:
24743599
[PubMed - in process]
Free PMC Article
5.

Complete Genome Sequence of a Multidrug-Resistant Salmonella enterica Serovar Typhimurium var. 5- Strain Isolated from Chicken Breast.

Hoffmann M, Muruvanda T, Allard MW, Korlach J, Roberts RJ, Timme R, Payne J, McDermott PF, Evans P, Meng J, Brown EW, Zhao S.

Genome Announc. 2014 Apr 3;2(2). pii: e00294-14. doi: 10.1128/genomeA.00294-14. No abstract available.

PMID:
24699967
[PubMed]
Free PMC Article
6.

Fully Assembled Genome Sequence for Salmonella enterica subsp. enterica Serovar Javiana CFSAN001992.

Allard MW, Muruvanda T, Strain E, Timme R, Luo Y, Wang C, Keys CE, Payne J, Cooper T, Luong K, Song Y, Chin CS, Korlach J, Roberts RJ, Evans P, Musser SM, Brown EW.

Genome Announc. 2014 Apr 3;2(2). pii: e00293-14. doi: 10.1128/genomeA.00293-14. No abstract available.

PMID:
24699966
[PubMed]
Free PMC Article
7.

Genome Sequence and Methylome of Soil Bacterium Gemmatirosa kalamazoonensis KBS708T, a Member of the Rarely Cultivated Gemmatimonadetes Phylum.

Debruyn JM, Radosevich M, Wommack KE, Polson SW, Hauser LJ, Fawaz MN, Korlach J, Tsai YC.

Genome Announc. 2014 Apr 3;2(2). pii: e00226-14. doi: 10.1128/genomeA.00226-14.

PMID:
24699952
[PubMed]
Free PMC Article
8.

Complete Closed Genome Sequences of Three Bibersteinia trehalosi Nasopharyngeal Isolates from Cattle with Shipping Fever.

Harhay GP, McVey DS, Koren S, Phillippy AM, Bono J, Harhay DM, Clawson ML, Heaton MP, Chitko-McKown CG, Korlach J, Smith TP.

Genome Announc. 2014 Feb 13;2(1). pii: e00084-14. doi: 10.1128/genomeA.00084-14.

PMID:
24526647
[PubMed]
Free PMC Article
9.

Novel giant siphovirus from Bacillus anthracis features unusual genome characteristics.

Ganz HH, Law C, Schmuki M, Eichenseher F, Calendar R, Loessner MJ, Getz WM, Korlach J, Beyer W, Klumpp J.

PLoS One. 2014 Jan 27;9(1):e85972. doi: 10.1371/journal.pone.0085972. eCollection 2014.

PMID:
24475065
[PubMed - in process]
Free PMC Article
10.

Reconstructing complex regions of genomes using long-read sequencing technology.

Huddleston J, Ranade S, Malig M, Antonacci F, Chaisson M, Hon L, Sudmant PH, Graves TA, Alkan C, Dennis MY, Wilson RK, Turner SW, Korlach J, Eichler EE.

Genome Res. 2014 Apr;24(4):688-96. doi: 10.1101/gr.168450.113. Epub 2014 Jan 13.

PMID:
24418700
[PubMed - in process]
11.

Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7.

Cooper KK, Mandrell RE, Louie JW, Korlach J, Clark TA, Parker CT, Huynh S, Chain PS, Ahmed S, Carter MQ.

BMC Genomics. 2014 Jan 10;15:17. doi: 10.1186/1471-2164-15-17.

PMID:
24410921
[PubMed - in process]
Free PMC Article
12.

Complete Genome Sequence of a Multidrug-Resistant Salmonella enterica Serovar Typhimurium var. 5- Strain Isolated from Chicken Breast.

Hoffmann M, Muruvanda T, Allard MW, Korlach J, Roberts RJ, Timme R, Payne J, McDermott PF, Evans P, Meng J, Brown EW, Zhao S.

Genome Announc. 2013 Dec 19;1(6). pii: e01068-13. doi: 10.1128/genomeA.01068-13.

PMID:
24356834
[PubMed]
Free PMC Article
13.

The complex methylome of the human gastric pathogen Helicobacter pylori.

Krebes J, Morgan RD, Bunk B, Spröer C, Luong K, Parusel R, Anton BP, König C, Josenhans C, Overmann J, Roberts RJ, Korlach J, Suerbaum S.

Nucleic Acids Res. 2014 Feb;42(4):2415-32. doi: 10.1093/nar/gkt1201. Epub 2013 Dec 2.

PMID:
24302578
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Global methylation state at base-pair resolution of the Caulobacter genome throughout the cell cycle.

Kozdon JB, Melfi MD, Luong K, Clark TA, Boitano M, Wang S, Zhou B, Gonzalez D, Collier J, Turner SW, Korlach J, Shapiro L, McAdams HH.

Proc Natl Acad Sci U S A. 2013 Nov 26;110(48):E4658-67. doi: 10.1073/pnas.1319315110. Epub 2013 Nov 11.

PMID:
24218615
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Exploring the roles of DNA methylation in the metal-reducing bacterium Shewanella oneidensis MR-1.

Bendall ML, Luong K, Wetmore KM, Blow M, Korlach J, Deutschbauer A, Malmstrom RR.

J Bacteriol. 2013 Nov;195(21):4966-74. doi: 10.1128/JB.00935-13. Epub 2013 Aug 30.

PMID:
23995632
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.

Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J.

Nat Methods. 2013 Jun;10(6):563-9. doi: 10.1038/nmeth.2474. Epub 2013 May 5.

PMID:
23644548
[PubMed - indexed for MEDLINE]
17.

Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans.

Brotherton P, Haak W, Templeton J, Brandt G, Soubrier J, Jane Adler C, Richards SM, Sarkissian CD, Ganslmeier R, Friederich S, Dresely V, van Oven M, Kenyon R, Van der Hoek MB, Korlach J, Luong K, Ho SY, Quintana-Murci L, Behar DM, Meller H, Alt KW, Cooper A; Genographic Consortium, Adhikarla S, Ganesh Prasad AK, Pitchappan R, Varatharajan Santhakumari A, Balanovska E, Balanovsky O, Bertranpetit J, Comas D, Martínez-Cruz B, Melé M, Clarke AC, Matisoo-Smith EA, Dulik MC, Gaieski JB, Owings AC, Schurr TG, Vilar MG, Hobbs A, Soodyall H, Javed A, Parida L, Platt DE, Royyuru AK, Jin L, Li S, Kaplan ME, Merchant NC, John Mitchell R, Renfrew C, Lacerda DR, Santos FR, Soria Hernanz DF, Spencer Wells R, Swamikrishnan P, Tyler-Smith C, Paulo Vieira P, Ziegle JS.

Nat Commun. 2013;4:1764. doi: 10.1038/ncomms2656.

PMID:
23612305
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription.

Vilfan ID, Tsai YC, Clark TA, Wegener J, Dai Q, Yi C, Pan T, Turner SW, Korlach J.

J Nanobiotechnology. 2013 Apr 3;11:8. doi: 10.1186/1477-3155-11-8.

PMID:
23552456
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic.

Feng Z, Fang G, Korlach J, Clark T, Luong K, Zhang X, Wong W, Schadt E.

PLoS Comput Biol. 2013;9(3):e1002935. doi: 10.1371/journal.pcbi.1002935. Epub 2013 Mar 14.

PMID:
23516341
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Fully assembled genome sequence for Salmonella enterica subsp. enterica Serovar Javiana CFSAN001992.

Allard MW, Muruvanda T, Strain E, Timme R, Luo Y, Wang C, Keys CE, Payne J, Cooper T, Luong K, Song Y, Chin CS, Korlach J, Roberts RJ, Evans P, Musser SM, Brown EW.

Genome Announc. 2013 Mar 21;1(2):e0008113. doi: 10.1128/genomeA.00081-13.

PMID:
23516208
[PubMed]
Free PMC Article

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