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Items: 1 to 20 of 129

1.

Sequencing and de novo assembly of 150 genomes from Denmark as a population reference.

Maretty L, Jensen JM, Petersen B, Sibbesen JA, Liu S, Villesen P, Skov L, Belling K, Theil Have C, Izarzugaza JMG, Grosjean M, Bork-Jensen J, Grove J, Als TD, Huang S, Chang Y, Xu R, Ye W, Rao J, Guo X, Sun J, Cao H, Ye C, van Beusekom J, Espeseth T, Flindt E, Friborg RM, Halager AE, Le Hellard S, Hultman CM, Lescai F, Li S, Lund O, Løngren P, Mailund T, Matey-Hernandez ML, Mors O, Pedersen CNS, Sicheritz-Pontén T, Sullivan P, Syed A, Westergaard D, Yadav R, Li N, Xu X, Hansen T, Krogh A, Bolund L, Sørensen TIA, Pedersen O, Gupta R, Rasmussen S, Besenbacher S, Børglum AD, Wang J, Eiberg H, Kristiansen K, Brunak S, Schierup MH.

Nature. 2017 Aug 3;548(7665):87-91. doi: 10.1038/nature23264. Epub 2017 Jul 26.

PMID:
28746312
2.

De novo assembly and phasing of a Korean human genome.

Seo JS, Rhie A, Kim J, Lee S, Sohn MH, Kim CU, Hastie A, Cao H, Yun JY, Kim J, Kuk J, Park GH, Kim J, Ryu H, Kim J, Roh M, Baek J, Hunkapiller MW, Korlach J, Shin JY, Kim C.

Nature. 2016 Oct 13;538(7624):243-247. doi: 10.1038/nature20098. Epub 2016 Oct 5.

PMID:
27706134
3.

A map of human genome variation from population-scale sequencing.

1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA.

Nature. 2010 Oct 28;467(7319):1061-73. doi: 10.1038/nature09534. Erratum in: Nature. 2011 May 26;473(7348):544. Xue, Yali [added]; Cartwright, Reed A [added]; Altshuler, David L [corrected to Altshuler, David]; Kebbel, Andrew [corrected to Keebler, Jonathan]; Koko-Gonzales, Paula [corrected to Kokko-Gonzales, Paula]; Nickerson, Debbie A [corrected to Nickerson, Debo.

4.

A global reference for human genetic variation.

1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR.

Nature. 2015 Oct 1;526(7571):68-74. doi: 10.1038/nature15393.

5.

Assembly and analysis of 100 full MHC haplotypes from the Danish population.

Jensen JM, Villesen P, Friborg RM; Danish Pan-Genome Consortium, Mailund T, Besenbacher S, Schierup MH.

Genome Res. 2017 Sep;27(9):1597-1607. doi: 10.1101/gr.218891.116. Epub 2017 Aug 3.

6.

Genetic variation and the de novo assembly of human genomes.

Chaisson MJ, Wilson RK, Eichler EE.

Nat Rev Genet. 2015 Nov;16(11):627-40. doi: 10.1038/nrg3933. Epub 2015 Oct 7. Review.

7.

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.

8.

Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing.

Solares EA, Chakraborty M, Miller DE, Kalsow S, Hall K, Perera AG, Emerson JJ, Hawley RS.

G3 (Bethesda). 2018 Oct 3;8(10):3143-3154. doi: 10.1534/g3.118.200162.

9.

Whole genome sequencing.

Ng PC, Kirkness EF.

Methods Mol Biol. 2010;628:215-26. doi: 10.1007/978-1-60327-367-1_12. Review.

PMID:
20238084
10.

De novo human genome assemblies reveal spectrum of alternative haplotypes in diverse populations.

Wong KHY, Levy-Sakin M, Kwok PY.

Nat Commun. 2018 Aug 2;9(1):3040. doi: 10.1038/s41467-018-05513-w.

11.

An integrated map of structural variation in 2,504 human genomes.

Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA; 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO.

Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394.

12.

Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale.

Liu S, Huang S, Rao J, Ye W; Genome Denmark ConsortiumII, Krogh A, Wang J.

Gigascience. 2015 Dec 24;4:64. doi: 10.1186/s13742-015-0103-4. eCollection 2015.

13.

Anchored pseudo-de novo assembly of human genomes identifies extensive sequence variation from unmapped sequence reads.

Faber-Hammond JJ, Brown KH.

Hum Genet. 2016 Jul;135(7):727-40. doi: 10.1007/s00439-016-1667-5. Epub 2016 Apr 9.

14.

Structural Variation Detection and Analysis Using Bionano Optical Mapping.

Chan S, Lam E, Saghbini M, Bocklandt S, Hastie A, Cao H, Holmlin E, Borodkin M.

Methods Mol Biol. 2018;1833:193-203. doi: 10.1007/978-1-4939-8666-8_16.

PMID:
30039375
15.

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.

16.

Limitations of next-generation genome sequence assembly.

Alkan C, Sajjadian S, Eichler EE.

Nat Methods. 2011 Jan;8(1):61-5. doi: 10.1038/nmeth.1527. Epub 2010 Nov 21.

17.

NovoGraph: Human genome graph construction from multiple long-read de novo assemblies.

Biederstedt E, Oliver JC, Hansen NF, Jajoo A, Dunn N, Olson A, Busby B, Dilthey AT.

Version 2. F1000Res. 2018 Sep 3 [revised 2018 Jan 1];7:1391. doi: 10.12688/f1000research.15895.2. eCollection 2018.

18.

Comparative analysis of de novo assemblers for variation discovery in personal genomes.

Tian S, Yan H, Klee EW, Kalmbach M, Slager SL.

Brief Bioinform. 2018 Sep 28;19(5):893-904. doi: 10.1093/bib/bbx037.

19.

Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios.

Besenbacher S, Liu S, Izarzugaza JM, Grove J, Belling K, Bork-Jensen J, Huang S, Als TD, Li S, Yadav R, Rubio-García A, Lescai F, Demontis D, Rao J, Ye W, Mailund T, Friborg RM, Pedersen CN, Xu R, Sun J, Liu H, Wang O, Cheng X, Flores D, Rydza E, Rapacki K, Damm Sørensen J, Chmura P, Westergaard D, Dworzynski P, Sørensen TI, Lund O, Hansen T, Xu X, Li N, Bolund L, Pedersen O, Eiberg H, Krogh A, Børglum AD, Brunak S, Kristiansen K, Schierup MH, Wang J, Gupta R, Villesen P, Rasmussen S.

Nat Commun. 2015 Jan 19;6:5969. doi: 10.1038/ncomms6969.

20.

Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies.

Li M, Chen L, Tian S, Lin Y, Tang Q, Zhou X, Li D, Yeung CKL, Che T, Jin L, Fu Y, Ma J, Wang X, Jiang A, Lan J, Pan Q, Liu Y, Luo Z, Guo Z, Liu H, Zhu L, Shuai S, Tang G, Zhao J, Jiang Y, Bai L, Zhang S, Mai M, Li C, Wang D, Gu Y, Wang G, Lu H, Li Y, Zhu H, Li Z, Li M, Gladyshev VN, Jiang Z, Zhao S, Wang J, Li R, Li X.

Genome Res. 2017 May;27(5):865-874. doi: 10.1101/gr.207456.116. Epub 2016 Sep 19.

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