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Results: 1 to 20 of 81

1.

A new rhesus macaque assembly and annotation for next-generation sequencing analyses.

Zimin AV, Cornish AS, Maudhoo MD, Gibbs RM, Zhang X, Pandey S, Meehan DT, Wipfler K, Bosinger SE, Johnson ZP, Tharp GK, Marçais G, Roberts M, Ferguson B, Fox HS, Treangen T, Salzberg SL, Yorke JA, Norgren RB Jr.

Biol Direct. 2014 Oct 14;9(1):20. doi: 10.1186/1745-6150-9-20.

PMID:
25319552
[PubMed - in process]
Free PMC Article
2.

Scaling of chaos versus periodicity: how certain is it that an attractor is chaotic?

Joglekar M, Ott E, Yorke JA.

Phys Rev Lett. 2014 Aug 22;113(8):084101. Epub 2014 Aug 20.

PMID:
25192099
[PubMed - in process]
3.

Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation.

Wegrzyn JL, Liechty JD, Stevens KA, Wu LS, Loopstra CA, Vasquez-Gross HA, Dougherty WM, Lin BY, Zieve JJ, Martínez-García PJ, Holt C, Yandell M, Zimin AV, Yorke JA, Crepeau MW, Puiu D, Salzberg SL, Dejong PJ, Mockaitis K, Main D, Langley CH, Neale DB.

Genetics. 2014 Mar;196(3):891-909. doi: 10.1534/genetics.113.159996.

PMID:
24653211
[PubMed - indexed for MEDLINE]
4.

Sequencing and assembly of the 22-gb loblolly pine genome.

Zimin A, Stevens KA, Crepeau MW, Holtz-Morris A, Koriabine M, Marçais G, Puiu D, Roberts M, Wegrzyn JL, de Jong PJ, Neale DB, Salzberg SL, Yorke JA, Langley CH.

Genetics. 2014 Mar;196(3):875-90. doi: 10.1534/genetics.113.159715.

PMID:
24653210
[PubMed - indexed for MEDLINE]
5.

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies.

Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, Puiu D, Crepeau MW, Cardeno C, Koriabine M, Holtz-Morris AE, Liechty JD, Martínez-García PJ, Vasquez-Gross HA, Lin BY, Zieve JJ, Dougherty WM, Fuentes-Soriano S, Wu LS, Gilbert D, Marçais G, Roberts M, Holt C, Yandell M, Davis JM, Smith KE, Dean JF, Lorenz WW, Whetten RW, Sederoff R, Wheeler N, McGuire PE, Main D, Loopstra CA, Mockaitis K, deJong PJ, Yorke JA, Salzberg SL, Langley CH.

Genome Biol. 2014 Mar 4;15(3):R59. doi: 10.1186/gb-2014-15-3-r59.

PMID:
24647006
[PubMed - in process]
Free PMC Article
6.

A period-doubling cascade precedes chaos for planar maps.

Sander E, Yorke JA.

Chaos. 2013 Sep;23(3):033113. doi: 10.1063/1.4813600.

PMID:
24089949
[PubMed]
7.

The MaSuRCA genome assembler.

Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA.

Bioinformatics. 2013 Nov 1;29(21):2669-77. doi: 10.1093/bioinformatics/btt476. Epub 2013 Aug 29.

PMID:
23990416
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Dynamics of partial control.

Sabuco J, Sanjuán MA, Yorke JA.

Chaos. 2012 Dec;22(4):047507. doi: 10.1063/1.4754874.

PMID:
23278093
[PubMed]
9.

Tailoring an alien ferredoxin to support native-like P450 monooxygenase activity.

Bell SG, McMillan JH, Yorke JA, Kavanagh E, Johnson EO, Wong LL.

Chem Commun (Camb). 2012 Dec 11;48(95):11692-4. doi: 10.1039/c2cc35968e.

PMID:
23104016
[PubMed - indexed for MEDLINE]
10.

Mis-assembled "segmental duplications" in two versions of the Bos taurus genome.

Zimin AV, Kelley DR, Roberts M, Marçais G, Salzberg SL, Yorke JA.

PLoS One. 2012;7(8):e42680. doi: 10.1371/journal.pone.0042680. Epub 2012 Aug 3.

PMID:
22880081
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Structure and function of CYP108D1 from Novosphingobium aromaticivorans DSM12444: an aromatic hydrocarbon-binding P450 enzyme.

Bell SG, Yang W, Yorke JA, Zhou W, Wang H, Harmer J, Copley R, Zhang A, Zhou R, Bartlam M, Rao Z, Wong LL.

Acta Crystallogr D Biol Crystallogr. 2012 Mar;68(Pt 3):277-91. doi: 10.1107/S090744491200145X. Epub 2012 Feb 14.

PMID:
22349230
[PubMed - indexed for MEDLINE]
12.

GAGE: A critical evaluation of genome assemblies and assembly algorithms.

Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marçais G, Pop M, Yorke JA.

Genome Res. 2012 Mar;22(3):557-67. doi: 10.1101/gr.131383.111. Epub 2012 Jan 6. Erratum in: Genome Res. 2012 Jun;22(6):1196.

PMID:
22147368
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Chain length-dependent cooperativity in fatty acid binding and oxidation by cytochrome P450BM3 (CYP102A1).

Rowlatt B, Yorke JA, Strong AJ, Whitehouse CJ, Bell SG, Wong LL.

Protein Cell. 2011 Aug;2(8):656-71. doi: 10.1007/s13238-011-1082-6. Epub 2011 Sep 9.

PMID:
21904981
[PubMed - indexed for MEDLINE]
14.

Structure, electronic properties and catalytic behaviour of an activity-enhancing CYP102A1 (P450(BM3)) variant.

Whitehouse CJ, Yang W, Yorke JA, Tufton HG, Ogilvie LC, Bell SG, Zhou W, Bartlam M, Rao Z, Wong LL.

Dalton Trans. 2011 Oct 28;40(40):10383-96. doi: 10.1039/c1dt10098j. Epub 2011 May 20.

PMID:
21603690
[PubMed - indexed for MEDLINE]
15.

Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile).

Smith CD, Zimin A, Holt C, Abouheif E, Benton R, Cash E, Croset V, Currie CR, Elhaik E, Elsik CG, Fave MJ, Fernandes V, Gadau J, Gibson JD, Graur D, Grubbs KJ, Hagen DE, Helmkampf M, Holley JA, Hu H, Viniegra AS, Johnson BR, Johnson RM, Khila A, Kim JW, Laird J, Mathis KA, Moeller JA, Muñoz-Torres MC, Murphy MC, Nakamura R, Nigam S, Overson RP, Placek JE, Rajakumar R, Reese JT, Robertson HM, Smith CR, Suarez AV, Suen G, Suhr EL, Tao S, Torres CW, van Wilgenburg E, Viljakainen L, Walden KK, Wild AL, Yandell M, Yorke JA, Tsutsui ND.

Proc Natl Acad Sci U S A. 2011 Apr 5;108(14):5673-8. doi: 10.1073/pnas.1008617108. Epub 2011 Jan 31.

PMID:
21282631
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Structural basis for the properties of two single-site proline mutants of CYP102A1 (P450BM3).

Whitehouse CJ, Yang W, Yorke JA, Rowlatt BC, Strong AJ, Blanford CF, Bell SG, Bartlam M, Wong LL, Rao Z.

Chembiochem. 2010 Dec 10;11(18):2549-56. doi: 10.1002/cbic.201000421.

PMID:
21110374
[PubMed - indexed for MEDLINE]
17.

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.

Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg Le Ann, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, Dong JJ, Evans C, Frederickson KM, Flicek P, Florea L, Folkerts O, Groenen MA, Harkins TT, Herrero J, Hoffmann S, Megens HJ, Jiang A, de Jong P, Kaiser P, Kim H, Kim KW, Kim S, Langenberger D, Lee MK, Lee T, Mane S, Marcais G, Marz M, McElroy AP, Modise T, Nefedov M, Notredame C, Paton IR, Payne WS, Pertea G, Prickett D, Puiu D, Qioa D, Raineri E, Ruffier M, Salzberg SL, Schatz MC, Scheuring C, Schmidt CJ, Schroeder S, Searle SM, Smith EJ, Smith J, Sonstegard TS, Stadler PF, Tafer H, Tu ZJ, Van Tassell CP, Vilella AJ, Williams KP, Yorke JA, Zhang L, Zhang HB, Zhang X, Zhang Y, Reed KM.

PLoS Biol. 2010 Sep 7;8(9). pii: e1000475. doi: 10.1371/journal.pbio.1000475.

PMID:
20838655
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

A highly active single-mutation variant of P450BM3 (CYP102A1).

Whitehouse CJ, Bell SG, Yang W, Yorke JA, Blanford CF, Strong AJ, Morse EJ, Bartlam M, Rao Z, Wong LL.

Chembiochem. 2009 Jul 6;10(10):1654-6. doi: 10.1002/cbic.200900279.

PMID:
19492389
[PubMed - indexed for MEDLINE]
19.

A whole-genome assembly of the domestic cow, Bos taurus.

Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F, Pertea G, Van Tassell CP, Sonstegard TS, Marçais G, Roberts M, Subramanian P, Yorke JA, Salzberg SL.

Genome Biol. 2009;10(4):R42. doi: 10.1186/gb-2009-10-4-r42. Epub 2009 Apr 24.

PMID:
19393038
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Duplication count distributions in DNA sequences.

Sindi SS, Hunt BR, Yorke JA.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Dec;78(6 Pt 1):061912. Epub 2008 Dec 11.

PMID:
19256873
[PubMed - indexed for MEDLINE]
Free PMC Article

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