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Items: 1 to 50 of 130

1.

Genomic Variation Among and Within Six Juglans Species.

Stevens KA, Woeste K, Chakraborty S, Crepeau MW, Leslie CA, Martínez-García PJ, Puiu D, Romero-Severson J, Coggeshall M, Dandekar AM, Kluepfel D, Neale DB, Salzberg SL, Langley CH.

G3 (Bethesda). 2018 Jul 2;8(7):2153-2165. doi: 10.1534/g3.118.200030.

2.

Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.

Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB, Salzberg SL.

Gigascience. 2017 Oct 1;6(10):1. doi: 10.1093/gigascience/gix072.

3.

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae.

Neale DB, McGuire PE, Wheeler NC, Stevens KA, Crepeau MW, Cardeno C, Zimin AV, Puiu D, Pertea GM, Sezen UU, Casola C, Koralewski TE, Paul R, Gonzalez-Ibeas D, Zaman S, Cronn R, Yandell M, Holt C, Langley CH, Yorke JA, Salzberg SL, Wegrzyn JL.

G3 (Bethesda). 2017 Sep 7;7(9):3157-3167. doi: 10.1534/g3.117.300078.

4.

An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.

Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB, Salzberg SL.

Gigascience. 2017 Jan 1;6(1):1-4. doi: 10.1093/gigascience/giw016. Erratum in: Gigascience. 2017 Oct 1;6(10):1.

5.

From Pine Cones to Read Clouds: Rescaffolding the Megagenome of Sugar Pine (Pinus lambertiana).

Crepeau MW, Langley CH, Stevens KA.

G3 (Bethesda). 2017 May 5;7(5):1563-1568. doi: 10.1534/g3.117.040055.

6.

Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana).

Gonzalez-Ibeas D, Martinez-Garcia PJ, Famula RA, Delfino-Mix A, Stevens KA, Loopstra CA, Langley CH, Neale DB, Wegrzyn JL.

G3 (Bethesda). 2016 Dec 7;6(12):3787-3802. doi: 10.1534/g3.116.032805.

7.

Sequence of the Sugar Pine Megagenome.

Stevens KA, Wegrzyn JL, Zimin A, Puiu D, Crepeau M, Cardeno C, Paul R, Gonzalez-Ibeas D, Koriabine M, Holtz-Morris AE, Martínez-García PJ, Sezen UU, Marçais G, Jermstad K, McGuire PE, Loopstra CA, Davis JM, Eckert A, de Jong P, Yorke JA, Salzberg SL, Neale DB, Langley CH.

Genetics. 2016 Dec;204(4):1613-1626. Epub 2016 Oct 28.

8.

First Draft Assembly and Annotation of the Genome of a California Endemic Oak Quercus lobata Née (Fagaceae).

Sork VL, Fitz-Gibbon ST, Puiu D, Crepeau M, Gugger PF, Sherman R, Stevens K, Langley CH, Pellegrini M, Salzberg SL.

G3 (Bethesda). 2016 Sep 12. pii: g3.116.030411. doi: 10.1534/g3.116.030411. [Epub ahead of print]

9.

Hubby and Lewontin on Protein Variation in Natural Populations: When Molecular Genetics Came to the Rescue of Population Genetics.

Charlesworth B, Charlesworth D, Coyne JA, Langley CH.

Genetics. 2016 Aug;203(4):1497-503. doi: 10.1534/genetics.115.185975.

10.

The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols.

Martínez-García PJ, Crepeau MW, Puiu D, Gonzalez-Ibeas D, Whalen J, Stevens KA, Paul R, Butterfield TS, Britton MT, Reagan RL, Chakraborty S, Walawage SL, Vasquez-Gross HA, Cardeno C, Famula RA, Pratt K, Kuruganti S, Aradhya MK, Leslie CA, Dandekar AM, Salzberg SL, Wegrzyn JL, Langley CH, Neale DB.

Plant J. 2016 Sep;87(5):507-32. doi: 10.1111/tpj.13207. Epub 2016 Jul 18.

11.

The Drosophila genome nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population.

Lack JB, Cardeno CM, Crepeau MW, Taylor W, Corbett-Detig RB, Stevens KA, Langley CH, Pool JE.

Genetics. 2015 Apr;199(4):1229-41. doi: 10.1534/genetics.115.174664. Epub 2015 Jan 27.

12.

Nucleosomes shape DNA polymorphism and divergence.

Langley SA, Karpen GH, Langley CH.

PLoS Genet. 2014 Jul 3;10(7):e1004457. doi: 10.1371/journal.pgen.1004457. eCollection 2014 Jul.

13.

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.

14.

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.

15.

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.

16.

Differential strengths of positive selection revealed by hitchhiking effects at small physical scales in Drosophila melanogaster.

Lee YC, Langley CH, Begun DJ.

Mol Biol Evol. 2014 Apr;31(4):804-16. doi: 10.1093/molbev/mst270. Epub 2013 Dec 20.

17.

The evolutionary genetics of the genes underlying phenotypic associations for loblolly pine (Pinus taeda, Pinaceae).

Eckert AJ, Wegrzyn JL, Liechty JD, Lee JM, Cumbie WP, Davis JM, Goldfarb B, Loopstra CA, Palle SR, Quesada T, Langley CH, Neale DB.

Genetics. 2013 Dec;195(4):1353-72. doi: 10.1534/genetics.113.157198. Epub 2013 Oct 11.

18.

Insights into the loblolly pine genome: characterization of BAC and fosmid sequences.

Wegrzyn JL, Lin BY, Zieve JJ, Dougherty WM, Martínez-García PJ, Koriabine M, Holtz-Morris A, deJong P, Crepeau M, Langley CH, Puiu D, Salzberg SL, Neale DB, Stevens KA.

PLoS One. 2013 Sep 4;8(9):e72439. doi: 10.1371/journal.pone.0072439. eCollection 2013.

19.

Open access to tree genomes: the path to a better forest.

Neale DB, Langley CH, Salzberg SL, Wegrzyn JL.

Genome Biol. 2013 Jun 24;14(6):120. doi: 10.1186/gb-2013-14-6-120.

20.

Population Genomics of sub-saharan Drosophila melanogaster: African diversity and non-African admixture.

Pool JE, Corbett-Detig RB, Sugino RP, Stevens KA, Cardeno CM, Crepeau MW, Duchen P, Emerson JJ, Saelao P, Begun DJ, Langley CH.

PLoS Genet. 2012;8(12):e1003080. doi: 10.1371/journal.pgen.1003080. Epub 2012 Dec 20.

21.

Population genomic analysis of base composition evolution in Drosophila melanogaster.

Poh YP, Ting CT, Fu HW, Langley CH, Begun DJ.

Genome Biol Evol. 2012;4(12):1245-55. doi: 10.1093/gbe/evs097.

22.

Long-term and short-term evolutionary impacts of transposable elements on Drosophila.

Lee YC, Langley CH.

Genetics. 2012 Dec;192(4):1411-32. doi: 10.1534/genetics.112.145714. Epub 2012 Sep 20.

23.

Sequence-based detection and breakpoint assembly of polymorphic inversions.

Corbett-Detig RB, Cardeno C, Langley CH.

Genetics. 2012 Sep;192(1):131-7. doi: 10.1534/genetics.112.141622. Epub 2012 Jun 5.

24.

Genomic variation in natural populations of Drosophila melanogaster.

Langley CH, Stevens K, Cardeno C, Lee YC, Schrider DR, Pool JE, Langley SA, Suarez C, Corbett-Detig RB, Kolaczkowski B, Fang S, Nista PM, Holloway AK, Kern AD, Dewey CN, Song YS, Hahn MW, Begun DJ.

Genetics. 2012 Oct;192(2):533-98. doi: 10.1534/genetics.112.142018. Epub 2012 Jun 5.

25.

Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster.

Schrider DR, Stevens K, Cardeño CM, Langley CH, Hahn MW.

Genome Res. 2011 Dec;21(12):2087-95. doi: 10.1101/gr.116434.110.

26.

Circumventing heterozygosity: sequencing the amplified genome of a single haploid Drosophila melanogaster embryo.

Langley CH, Crepeau M, Cardeno C, Corbett-Detig R, Stevens K.

Genetics. 2011 Jun;188(2):239-46. doi: 10.1534/genetics.111.127530. Epub 2011 Mar 24.

27.

On the genealogy of asexual diploids.

Lam F, Langley CH, Song YS.

J Comput Biol. 2011 Mar;18(3):415-28. doi: 10.1089/cmb.2010.0270.

28.

Evolution of disease response genes in loblolly pine: insights from candidate genes.

Ersoz ES, Wright MH, González-Martínez SC, Langley CH, Neale DB.

PLoS One. 2010 Dec 6;5(12):e14234. doi: 10.1371/journal.pone.0014234.

29.

The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences.

Kovach A, Wegrzyn JL, Parra G, Holt C, Bruening GE, Loopstra CA, Hartigan J, Yandell M, Langley CH, Korf I, Neale DB.

BMC Genomics. 2010 Jul 7;11:420. doi: 10.1186/1471-2164-11-420.

30.

Transposable elements in natural populations of Drosophila melanogaster.

Lee YC, Langley CH.

Philos Trans R Soc Lond B Biol Sci. 2010 Apr 27;365(1544):1219-28. doi: 10.1098/rstb.2009.0318. Review.

31.

Molecular population genetics and evolution of Drosophila meiosis genes.

Anderson JA, Gilliland WD, Langley CH.

Genetics. 2009 Jan;181(1):177-85. doi: 10.1534/genetics.108.093807. Epub 2008 Nov 3.

32.

A test for the role of natural selection in the stabilization of transposable element copy number in a population of Drosophila melanogaster.

Montgomery E, Charlesworth B, Langley CH.

Genet Res. 2007 Dec;89(5-6):435-45. doi: 10.1017/S0016672308009634. No abstract available.

PMID:
18976533
33.

Molecular population genetics of Drosophila subtelomeric DNA.

Anderson JA, Song YS, Langley CH.

Genetics. 2008 Jan;178(1):477-87. doi: 10.1534/genetics.107.083196.

34.
35.

Evolution of genes and genomes on the Drosophila phylogeny.

Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I.

Nature. 2007 Nov 8;450(7167):203-18.

PMID:
17994087
36.

Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans.

Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh YP, Hahn MW, Nista PM, Jones CD, Kern AD, Dewey CN, Pachter L, Myers E, Langley CH.

PLoS Biol. 2007 Nov 6;5(11):e310.

37.
38.

The hitchhiking effect on linkage disequilibrium between linked neutral loci.

Stephan W, Song YS, Langley CH.

Genetics. 2006 Apr;172(4):2647-63. Epub 2006 Feb 1.

39.

DNA sequence polymorphism and divergence at the erect wing and suppressor of sable loci of Drosophila melanogaster and D. simulans.

Braverman JM, Lazzaro BP, Aguadé M, Langley CH.

Genetics. 2005 Jul;170(3):1153-65. Epub 2005 Jun 8.

40.
41.

Evolutionary genomics: codon bias and selection on single genomes.

Hahn MW, Mezey JG, Begun DJ, Gillespie JH, Kern AD, Langley CH, Moyle LC.

Nature. 2005 Jan 20;433(7023):E5-6; discussion E7-8.

PMID:
15662370
42.

Comparing the linkage maps of the close relatives Arabidopsis lyrata and A. thaliana.

Kuittinen H, de Haan AA, Vogl C, Oikarinen S, Leppälä J, Koch M, Mitchell-Olds T, Langley CH, Savolainen O.

Genetics. 2004 Nov;168(3):1575-84.

43.

Nucleotide diversity and linkage disequilibrium in loblolly pine.

Brown GR, Gill GP, Kuntz RJ, Langley CH, Neale DB.

Proc Natl Acad Sci U S A. 2004 Oct 19;101(42):15255-60. Epub 2004 Oct 11.

44.

The maintenance of extreme amino acid diversity at the disease resistance gene, RPP13, in Arabidopsis thaliana.

Rose LE, Bittner-Eddy PD, Langley CH, Holub EB, Michelmore RW, Beynon JL.

Genetics. 2004 Mar;166(3):1517-27.

45.

hairy: A quantitative trait locus for drosophila sensory bristle number.

Robin C, Lyman RF, Long AD, Langley CH, Mackay TF.

Genetics. 2002 Sep;162(1):155-64.

46.

Linkage disequilibria and the site frequency spectra in the su(s) and su(w(a)) regions of the Drosophila melanogaster X chromosome.

Langley CH, Lazzaro BP, Phillips W, Heikkinen E, Braverman JM.

Genetics. 2000 Dec;156(4):1837-52.

48.
49.

Is the fast/slow allozyme variation at the Adh locus of Drosophila melanogaster an ancient balanced polymorphism?

Begun DJ, Betancourt AJ, Langley CH, Stephan W.

Mol Biol Evol. 1999 Dec;16(12):1816-9. No abstract available.

PMID:
10605124

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