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Items: 1 to 20 of 107

1.

A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0).

Kuderna LFK, Tomlinson C, Hillier LW, Tran A, Fiddes IT, Armstrong J, Laayouni H, Gordon D, Huddleston J, Garcia Perez R, Povolotskaya I, Serres Armero A, Gómez Garrido J, Ho D, Ribeca P, Alioto T, Green RE, Paten B, Navarro A, Betranpetit J, Herrero J, Eichler EE, Sharp AJ, Feuk L, Warren WC, Marques-Bonet T.

Gigascience. 2017 Nov 1;6(11):1-6. doi: 10.1093/gigascience/gix098.

2.

Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity.

Low WY, Tearle R, Bickhart DM, Rosen BD, Kingan SB, Swale T, Thibaud-Nissen F, Murphy TD, Young R, Lefevre L, Hume DA, Collins A, Ajmone-Marsan P, Smith TPL, Williams JL.

Nat Commun. 2019 Jan 16;10(1):260. doi: 10.1038/s41467-018-08260-0.

3.

De novo assembly of the chimpanzee transcriptome from NextGen mRNA sequences.

Maudhoo MD, Madison JD, Norgren RB Jr.

Gigascience. 2015 Apr 18;4:18. doi: 10.1186/s13742-015-0061-x. eCollection 2015.

4.

Alignment of 1000 Genomes Project reads to reference assembly GRCh38.

Zheng-Bradley X, Streeter I, Fairley S, Richardson D, Clarke L, Flicek P; 1000 Genomes Project Consortium.

Gigascience. 2017 Jul 1;6(7):1-8. doi: 10.1093/gigascience/gix038.

5.

Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm.

Zimin AV, Puiu D, Luo MC, Zhu T, Koren S, Marçais G, Yorke JA, Dvořák J, Salzberg SL.

Genome Res. 2017 May;27(5):787-792. doi: 10.1101/gr.213405.116. Epub 2017 Jan 27.

6.

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.

Clavijo BJ, Venturini L, Schudoma C, Accinelli GG, Kaithakottil G, Wright J, Borrill P, Kettleborough G, Heavens D, Chapman H, Lipscombe J, Barker T, Lu FH, McKenzie N, Raats D, Ramirez-Gonzalez RH, Coince A, Peel N, Percival-Alwyn L, Duncan O, Trösch J, Yu G, Bolser DM, Namaati G, Kerhornou A, Spannagl M, Gundlach H, Haberer G, Davey RP, Fosker C, Palma FD, Phillips AL, Millar AH, Kersey PJ, Uauy C, Krasileva KV, Swarbreck D, Bevan MW, Clark MD.

Genome Res. 2017 May;27(5):885-896. doi: 10.1101/gr.217117.116.

7.

Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II.

Norman PJ, Norberg SJ, Guethlein LA, Nemat-Gorgani N, Royce T, Wroblewski EE, Dunn T, Mann T, Alicata C, Hollenbach JA, Chang W, Shults Won M, Gunderson KL, Abi-Rached L, Ronaghi M, Parham P.

Genome Res. 2017 May;27(5):813-823. doi: 10.1101/gr.213538.116. Epub 2017 Mar 30.

8.

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.

9.

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs.

Swain MT, Tsai IJ, Assefa SA, Newbold C, Berriman M, Otto TD.

Nat Protoc. 2012 Jun 7;7(7):1260-84. doi: 10.1038/nprot.2012.068.

10.

Reference transcriptome assembly and annotation for perennial ryegrass.

Shinozuka H, Cogan NOI, Spangenberg GC, Forster JW.

Genome. 2017 Dec;60(12):1086-1088. doi: 10.1139/gen-2017-0077. Epub 2017 Aug 25.

PMID:
28841400
11.

Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set.

Damas J, O'Connor R, Farré M, Lenis VPE, Martell HJ, Mandawala A, Fowler K, Joseph S, Swain MT, Griffin DK, Larkin DM.

Genome Res. 2017 May;27(5):875-884. doi: 10.1101/gr.213660.116. Epub 2016 Nov 30.

12.

ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter.

Jackman SD, Vandervalk BP, Mohamadi H, Chu J, Yeo S, Hammond SA, Jahesh G, Khan H, Coombe L, Warren RL, Birol I.

Genome Res. 2017 May;27(5):768-777. doi: 10.1101/gr.214346.116. Epub 2017 Feb 23.

13.

Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data.

Jiao WB, Accinelli GG, Hartwig B, Kiefer C, Baker D, Severing E, Willing EM, Piednoel M, Woetzel S, Madrid-Herrero E, Huettel B, Hümann U, Reinhard R, Koch MA, Swan D, Clavijo B, Coupland G, Schneeberger K.

Genome Res. 2017 May;27(5):778-786. doi: 10.1101/gr.213652.116. Epub 2017 Feb 3.

14.

U50: A New Metric for Measuring Assembly Output Based on Non-Overlapping, Target-Specific Contigs.

Castro CJ, Ng TFF.

J Comput Biol. 2017 Nov;24(11):1071-1080. doi: 10.1089/cmb.2017.0013. Epub 2017 Apr 18.

15.

Chromosome assembly of large and complex genomes using multiple references.

Kolmogorov M, Armstrong J, Raney BJ, Streeter I, Dunn M, Yang F, Odom D, Flicek P, Keane TM, Thybert D, Paten B, Pham S.

Genome Res. 2018 Nov;28(11):1720-1732. doi: 10.1101/gr.236273.118. Epub 2018 Oct 19.

16.

A New Reference Genome Assembly for the Microcrustacean Daphnia pulex.

Ye Z, Xu S, Spitze K, Asselman J, Jiang X, Ackerman MS, Lopez J, Harker B, Raborn RT, Thomas WK, Ramsdell J, Pfrender ME, Lynch M.

G3 (Bethesda). 2017 May 5;7(5):1405-1416. doi: 10.1534/g3.116.038638.

17.

A comprehensive analysis of chimpanzee (Pan troglodytes)-specific LINE-1 retrotransposons.

Lee S, Tang W, Liang P, Han K.

Gene. 2019 Apr 20;693:46-51. doi: 10.1016/j.gene.2019.01.022. Epub 2019 Jan 26.

PMID:
30690181
18.

Extensive error in the number of genes inferred from draft genome assemblies.

Denton JF, Lugo-Martinez J, Tucker AE, Schrider DR, Warren WC, Hahn MW.

PLoS Comput Biol. 2014 Dec 4;10(12):e1003998. doi: 10.1371/journal.pcbi.1003998. eCollection 2014 Dec.

19.

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.

Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, Fulton RS, Kremitzki M, Magrini V, Markovic C, McGrath S, Steinberg KM, Auger K, Chow W, Collins J, Harden G, Hubbard T, Pelan S, Simpson JT, Threadgold G, Torrance J, Wood JM, Clarke L, Koren S, Boitano M, Peluso P, Li H, Chin CS, Phillippy AM, Durbin R, Wilson RK, Flicek P, Eichler EE, Church DM.

Genome Res. 2017 May;27(5):849-864. doi: 10.1101/gr.213611.116. Epub 2017 Apr 10.

20.

Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis.

Sato K, Kuroki Y, Kumita W, Fujiyama A, Toyoda A, Kawai J, Iriki A, Sasaki E, Okano H, Sakakibara Y.

Sci Rep. 2015 Nov 20;5:16894. doi: 10.1038/srep16894.

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