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Items: 1 to 20 of 86

1.

The Atlantic salmon genome provides insights into rediploidization.

Lien S, Koop BF, Sandve SR, Miller JR, Kent MP, Nome T, Hvidsten TR, Leong JS, Minkley DR, Zimin A, Grammes F, Grove H, Gjuvsland A, Walenz B, Hermansen RA, von Schalburg K, Rondeau EB, Di Genova A, Samy JK, Olav Vik J, Vigeland MD, Caler L, Grimholt U, Jentoft S, Våge DI, de Jong P, Moen T, Baranski M, Palti Y, Smith DR, Yorke JA, Nederbragt AJ, Tooming-Klunderud A, Jakobsen KS, Jiang X, Fan D, Hu Y, Liberles DA, Vidal R, Iturra P, Jones SJ, Jonassen I, Maass A, Omholt SW, Davidson WS.

Nature. 2016 Apr 18;533(7602):200-5. doi: 10.1038/nature17164.

PMID:
27088604
2.

Testing for Basins of Wada.

Daza A, Wagemakers A, Sanjuán MA, Yorke JA.

Sci Rep. 2015 Nov 10;5:16579. doi: 10.1038/srep16579.

3.

Drug Oxidation by Cytochrome P450BM3 : Metabolite Synthesis and Discovering New P450 Reaction Types.

Ren X, Yorke JA, Taylor E, Zhang T, Zhou W, Wong LL.

Chemistry. 2015 Oct 12;21(42):15039-47. doi: 10.1002/chem.201502020. Epub 2015 Aug 27.

PMID:
26311271
4.

QuorUM: An Error Corrector for Illumina Reads.

Marçais G, Yorke JA, Zimin A.

PLoS One. 2015 Jun 17;10(6):e0130821. doi: 10.1371/journal.pone.0130821. eCollection 2015.

5.

Geometry of the edge of chaos in a low-dimensional turbulent shear flow model.

Joglekar M, Feudel U, Yorke JA.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 May;91(5):052903. Epub 2015 May 7.

PMID:
26066225
6.

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.

7.

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
8.

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.

9.

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.

10.

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.

11.

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
12.

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.

13.

Dynamics of partial control.

Sabuco J, Sanjuán MA, Yorke JA.

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

PMID:
23278093
14.

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
15.

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.

16.

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
17.

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.

18.

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.

19.

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
20.

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.

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