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Items: 1 to 20 of 128

1.

Haplotype-resolved genome sequencing of a Gujarati Indian individual.

Kitzman JO, Mackenzie AP, Adey A, Hiatt JB, Patwardhan RP, Sudmant PH, Ng SB, Alkan C, Qiu R, Eichler EE, Shendure J.

Nat Biotechnol. 2011 Jan;29(1):59-63. doi: 10.1038/nbt.1740. Epub 2010 Dec 19. Erratum in: Nat Biotechnol. 2011 May;29(5):459.

2.

De novo assembly of a haplotype-resolved human genome.

Cao H, Wu H, Luo R, Huang S, Sun Y, Tong X, Xie Y, Liu B, Yang H, Zheng H, Li J, Li B, Wang Y, Yang F, Sun P, Liu S, Gao P, Huang H, Sun J, Chen D, He G, Huang W, Huang Z, Li Y, Tellier LC, Liu X, Feng Q, Xu X, Zhang X, Bolund L, Krogh A, Kristiansen K, Drmanac R, Drmanac S, Nielsen R, Li S, Wang J, Yang H, Li Y, Wong GK, Wang J.

Nat Biotechnol. 2015 Jun;33(6):617-22. doi: 10.1038/nbt.3200. Epub 2015 May 25.

PMID:
26006006
3.

Whole-genome haplotyping by dilution, amplification, and sequencing.

Kaper F, Swamy S, Klotzle B, Munchel S, Cottrell J, Bibikova M, Chuang HY, Kruglyak S, Ronaghi M, Eberle MA, Fan JB.

Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5552-7. doi: 10.1073/pnas.1218696110. Epub 2013 Mar 18.

4.

Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing.

Amini S, Pushkarev D, Christiansen L, Kostem E, Royce T, Turk C, Pignatelli N, Adey A, Kitzman JO, Vijayan K, Ronaghi M, Shendure J, Gunderson KL, Steemers FJ.

Nat Genet. 2014 Dec;46(12):1343-9. doi: 10.1038/ng.3119. Epub 2014 Oct 19.

5.

The diploid genome sequence of an Asian individual.

Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Zhang J, Guo Y, Feng B, Li H, Lu Y, Fang X, Liang H, Du Z, Li D, Zhao Y, Hu Y, Yang Z, Zheng H, Hellmann I, Inouye M, Pool J, Yi X, Zhao J, Duan J, Zhou Y, Qin J, Ma L, Li G, Yang Z, Zhang G, Yang B, Yu C, Liang F, Li W, Li S, Li D, Ni P, Ruan J, Li Q, Zhu H, Liu D, Lu Z, Li N, Guo G, Zhang J, Ye J, Fang L, Hao Q, Chen Q, Liang Y, Su Y, San A, Ping C, Yang S, Chen F, Li L, Zhou K, Zheng H, Ren Y, Yang L, Gao Y, Yang G, Li Z, Feng X, Kristiansen K, Wong GK, Nielsen R, Durbin R, Bolund L, Zhang X, Li S, Yang H, Wang J.

Nature. 2008 Nov 6;456(7218):60-5. doi: 10.1038/nature07484.

6.

A Fosmid Pool-Based Next Generation Sequencing Approach to Haplotype-Resolve Whole Genomes.

Suk EK, Schulz S, Mentrup B, Huebsch T, Duitama J, Hoehe MR.

Methods Mol Biol. 2017;1551:223-269. doi: 10.1007/978-1-4939-6750-6_13.

PMID:
28138850
7.

Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data.

Yang WY, Hormozdiari F, Wang Z, He D, Pasaniuc B, Eskin E.

Bioinformatics. 2013 Sep 15;29(18):2245-52. doi: 10.1093/bioinformatics/btt386. Epub 2013 Jul 3.

8.

WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads.

Patterson M, Marschall T, Pisanti N, van Iersel L, Stougie L, Klau GW, Schönhuth A.

J Comput Biol. 2015 Jun;22(6):498-509. doi: 10.1089/cmb.2014.0157. Epub 2015 Feb 6.

9.

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
10.

Haplotype-resolved genome sequencing: experimental methods and applications.

Snyder MW, Adey A, Kitzman JO, Shendure J.

Nat Rev Genet. 2015 Jun;16(6):344-58. doi: 10.1038/nrg3903. Epub 2015 May 7. Review.

PMID:
25948246
11.

Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing.

Selvaraj S, R Dixon J, Bansal V, Ren B.

Nat Biotechnol. 2013 Dec;31(12):1111-8. doi: 10.1038/nbt.2728. Epub 2013 Nov 3.

12.

Haplotype sorting using human fosmid clone end-sequence pairs.

Kidd JM, Cheng Z, Graves T, Fulton B, Wilson RK, Eichler EE.

Genome Res. 2008 Dec;18(12):2016-23. doi: 10.1101/gr.081786.108. Epub 2008 Oct 3.

13.

Targeted, haplotype-resolved resequencing of long segments of the human genome.

Raymond CK, Subramanian S, Paddock M, Qiu R, Deodato C, Palmieri A, Chang J, Radke T, Haugen E, Kas A, Waring D, Bovee D, Stacy R, Kaul R, Olson MV.

Genomics. 2005 Dec;86(6):759-66. Epub 2005 Oct 24.

14.

Decoding Genetic Variations: Communications-Inspired Haplotype Assembly.

Puljiz Z, Vikalo H.

IEEE/ACM Trans Comput Biol Bioinform. 2016 May-Jun;13(3):518-30. doi: 10.1109/TCBB.2015.2462367.

PMID:
27295635
15.

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing.

Zheng GX, Lau BT, Schnall-Levin M, Jarosz M, Bell JM, Hindson CM, Kyriazopoulou-Panagiotopoulou S, Masquelier DA, Merrill L, Terry JM, Mudivarti PA, Wyatt PW, Bharadwaj R, Makarewicz AJ, Li Y, Belgrader P, Price AD, Lowe AJ, Marks P, Vurens GM, Hardenbol P, Montesclaros L, Luo M, Greenfield L, Wong A, Birch DE, Short SW, Bjornson KP, Patel P, Hopmans ES, Wood C, Kaur S, Lockwood GK, Stafford D, Delaney JP, Wu I, Ordonez HS, Grimes SM, Greer S, Lee JY, Belhocine K, Giorda KM, Heaton WH, McDermott GP, Bent ZW, Meschi F, Kondov NO, Wilson R, Bernate JA, Gauby S, Kindwall A, Bermejo C, Fehr AN, Chan A, Saxonov S, Ness KD, Hindson BJ, Ji HP.

Nat Biotechnol. 2016 Mar;34(3):303-11. doi: 10.1038/nbt.3432. Epub 2016 Feb 1.

16.

Haplotype phasing of whole human genomes using bead-based barcode partitioning in a single tube.

Zhang F, Christiansen L, Thomas J, Pokholok D, Jackson R, Morrell N, Zhao Y, Wiley M, Welch E, Jaeger E, Granat A, Norberg SJ, Halpern A, C Rogert M, Ronaghi M, Shendure J, Gormley N, Gunderson KL, Steemers FJ.

Nat Biotechnol. 2017 Sep;35(9):852-857. doi: 10.1038/nbt.3897. Epub 2017 Jun 26.

PMID:
28650462
17.

Assembly and diploid architecture of an individual human genome via single-molecule technologies.

Pendleton M, Sebra R, Pang AW, Ummat A, Franzen O, Rausch T, Stütz AM, Stedman W, Anantharaman T, Hastie A, Dai H, Fritz MH, Cao H, Cohain A, Deikus G, Durrett RE, Blanchard SC, Altman R, Chin CS, Guo Y, Paxinos EE, Korbel JO, Darnell RB, McCombie WR, Kwok PY, Mason CE, Schadt EE, Bashir A.

Nat Methods. 2015 Aug;12(8):780-6. doi: 10.1038/nmeth.3454. Epub 2015 Jun 29.

18.

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, Deborah A].

19.

Sequencing and analysis of a South Asian-Indian personal genome.

Gupta R, Ratan A, Rajesh C, Chen R, Kim HL, Burhans R, Miller W, Santhosh S, Davuluri RV, Butte AJ, Schuster SC, Seshagiri S, Thomas G.

BMC Genomics. 2012 Aug 31;13:440. doi: 10.1186/1471-2164-13-440.

20.

Modeling Human Population Separation History Using Physically Phased Genomes.

Song S, Sliwerska E, Emery S, Kidd JM.

Genetics. 2017 Jan;205(1):385-395. doi: 10.1534/genetics.116.192963. Epub 2016 Nov 9.

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