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Items: 1 to 20 of 81

1.

AgIn: measuring the landscape of CpG methylation of individual repetitive elements.

Suzuki Y, Korlach J, Turner SW, Tsukahara T, Taniguchi J, Qu W, Ichikawa K, Yoshimura J, Yurino H, Takahashi Y, Mitsui J, Ishiura H, Tsuji S, Takeda H, Morishita S.

Bioinformatics. 2016 Jun 17. pii: btw360. [Epub ahead of print]

2.

Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding.

Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA, Van Heusden P, Singh S, Thevasagayam NM, Prakki SR, Purushothaman K, Saju JM, Jiang J, Mbandi SK, Jonas M, Hin Yan Tong A, Mwangi S, Lau D, Ngoh SY, Liew WC, Shen X, Hon LS, Drake JP, Boitano M, Hall R, Chin CS, Lachumanan R, Korlach J, Trifonov V, Kabilov M, Tupikin A, Green D, Moxon S, Garvin T, Sedlazeck FJ, Vurture GW, Gopalapillai G, Kumar Katneni V, Noble TH, Scaria V, Sivasubbu S, Jerry DR, O'Brien SJ, Schatz MC, Dalmay T, Turner SW, Lok S, Christoffels A, Orbán L.

PLoS Genet. 2016 Apr 15;12(4):e1005954. doi: 10.1371/journal.pgen.1005954. eCollection 2016 Apr.

3.

The Epigenomic Landscape of Prokaryotes.

Blow MJ, Clark TA, Daum CG, Deutschbauer AM, Fomenkov A, Fries R, Froula J, Kang DD, Malmstrom RR, Morgan RD, Posfai J, Singh K, Visel A, Wetmore K, Zhao Z, Rubin EM, Korlach J, Pennacchio LA, Roberts RJ.

PLoS Genet. 2016 Feb 12;12(2):e1005854. doi: 10.1371/journal.pgen.1005854. eCollection 2016 Feb. Erratum in: PLoS Genet. 2016 May;12(5):e1006064.

4.

Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing.

Tsai YC, Conlan S, Deming C; NISC Comparative Sequencing Program, Segre JA, Kong HH, Korlach J, Oh J.

MBio. 2016 Feb 9;7(1):e01948-15. doi: 10.1128/mBio.01948-15.

5.

Complete Genome Sequence of Streptomyces sp. Strain CCM_MD2014, Isolated from Topsoil in Woods Hole, Massachusetts.

Mariita RM, Bhatnagar S, Hanselmann K, Hossain MJ, Korlach J, Boitano M, Roberts RJ, Liles MR, Moss AG, Leadbetter JR, Newman DK, Dawson SC.

Genome Announc. 2015 Dec 31;3(6). pii: e01506-15. doi: 10.1128/genomeA.01506-15.

6.

Complete Genome Sequence of Curtobacterium sp. Strain MR_MD2014, Isolated from Topsoil in Woods Hole, Massachusetts.

Mariita RM, Bhatnagar S, Hanselmann K, Hossain MJ, Korlach J, Boitano M, Roberts RJ, Liles MR, Moss AG, Leadbetter JR, Newman DK, Dawson SC.

Genome Announc. 2015 Dec 31;3(6). pii: e01504-15. doi: 10.1128/genomeA.01504-15.

7.

DNA Methylation Assessed by SMRT Sequencing Is Linked to Mutations in Neisseria meningitidis Isolates.

Sater MR, Lamelas A, Wang G, Clark TA, Röltgen K, Mane S, Korlach J, Pluschke G, Schmid CD.

PLoS One. 2015 Dec 11;10(12):e0144612. doi: 10.1371/journal.pone.0144612. eCollection 2015.

8.

Enzymatic Degradation of Phenazines Can Generate Energy and Protect Sensitive Organisms from Toxicity.

Costa KC, Bergkessel M, Saunders S, Korlach J, Newman DK.

MBio. 2015 Oct 27;6(6):e01520-15. doi: 10.1128/mBio.01520-15.

9.

Returning to more finished genomes.

Korlach J.

Genom Data. 2014 Mar 1;2:46-8. doi: 10.1016/j.gdata.2014.02.003. eCollection 2014 Dec.

10.

A biphasic epigenetic switch controls immunoevasion, virulence and niche adaptation in non-typeable Haemophilus influenzae.

Atack JM, Srikhanta YN, Fox KL, Jurcisek JA, Brockman KL, Clark TA, Boitano M, Power PM, Jen FE, McEwan AG, Grimmond SM, Smith AL, Barenkamp SJ, Korlach J, Bakaletz LO, Jennings MP.

Nat Commun. 2015 Jul 28;6:7828. doi: 10.1038/ncomms8828.

11.

Genetic Stabilization of the Drug-Resistant PMEN1 Pneumococcus Lineage by Its Distinctive DpnIII Restriction-Modification System.

Eutsey RA, Powell E, Dordel J, Salter SJ, Clark TA, Korlach J, Ehrlich GD, Hiller NL.

MBio. 2015 Jun 16;6(3):e00173. doi: 10.1128/mBio.00173-15.

12.

Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing.

Weirather JL, Afshar PT, Clark TA, Tseng E, Powers LS, Underwood JG, Zabner J, Korlach J, Wong WH, Au KF.

Nucleic Acids Res. 2015 Oct 15;43(18):e116. doi: 10.1093/nar/gkv562. Epub 2015 Jun 3.

13.

Genome-wide methylation patterns in Salmonella enterica Subsp. enterica Serovars.

Pirone-Davies C, Hoffmann M, Roberts RJ, Muruvanda T, Timme RE, Strain E, Luo Y, Payne J, Luong K, Song Y, Tsai YC, Boitano M, Clark TA, Korlach J, Evans PS, Allard MW.

PLoS One. 2015 Apr 10;10(4):e0123639. doi: 10.1371/journal.pone.0123639. eCollection 2015.

14.

Specificity of the ModA11, ModA12 and ModD1 epigenetic regulator N(6)-adenine DNA methyltransferases of Neisseria meningitidis.

Seib KL, Jen FE, Tan A, Scott AL, Kumar R, Power PM, Chen LT, Wu HJ, Wang AH, Hill DM, Luyten YA, Morgan RD, Roberts RJ, Maiden MC, Boitano M, Clark TA, Korlach J, Rao DN, Jennings MP.

Nucleic Acids Res. 2015 Apr 30;43(8):4150-62. doi: 10.1093/nar/gkv219. Epub 2015 Apr 6.

15.

Complete Genome Sequence of the Hypervirulent Bacterium Clostridium difficile Strain G46, Ribotype 027.

Gaulton T, Misra R, Rose G, Baybayan P, Hall R, Freeman J, Turton J, Picton S, Korlach J, Gharbia S, Shah H.

Genome Announc. 2015 Mar 26;3(2). pii: e00073-15. doi: 10.1128/genomeA.00073-15.

16.

Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing.

Genest PA, Baugh L, Taipale A, Zhao W, Jan S, van Luenen HG, Korlach J, Clark T, Luong K, Boitano M, Turner S, Myler PJ, Borst P.

Nucleic Acids Res. 2015 Feb 27;43(4):2102-15. doi: 10.1093/nar/gkv095. Epub 2015 Feb 6.

17.

Complete Genome Sequence of a Klebsiella pneumoniae Isolate with Chromosomally Encoded Carbapenem Resistance and Colibactin Synthesis Loci.

Conlan S, Deming C, Tsai YC, Lau AF, Dekker JP, Korlach J, Segre JA.

Genome Announc. 2014 Dec 24;2(6). pii: e01332-14. doi: 10.1128/genomeA.01332-14.

18.

Genome annotation provides insight into carbon monoxide and hydrogen metabolism in Rubrivivax gelatinosus.

Wawrousek K, Noble S, Korlach J, Chen J, Eckert C, Yu J, Maness PC.

PLoS One. 2014 Dec 5;9(12):e114551. doi: 10.1371/journal.pone.0114551. eCollection 2014.

19.

Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP dioxygenases in Coprinopsis cinerea.

Chavez L, Huang Y, Luong K, Agarwal S, Iyer LM, Pastor WA, Hench VK, Frazier-Bowers SA, Korol E, Liu S, Tahiliani M, Wang Y, Clark TA, Korlach J, Pukkila PJ, Aravind L, Rao A.

Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):E5149-58. doi: 10.1073/pnas.1419513111. Epub 2014 Nov 18.

20.

Resolving the complexity of the human genome using single-molecule sequencing.

Chaisson MJ, Huddleston J, Dennis MY, Sudmant PH, Malig M, Hormozdiari F, Antonacci F, Surti U, Sandstrom R, Boitano M, Landolin JM, Stamatoyannopoulos JA, Hunkapiller MW, Korlach J, Eichler EE.

Nature. 2015 Jan 29;517(7536):608-11. doi: 10.1038/nature13907. Epub 2014 Nov 10.

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