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Items: 9

1.

Discovery and genotyping of structural variation from long-read haploid genome sequence data.

Huddleston J, Chaisson MJP, Steinberg KM, Warren W, Hoekzema K, Gordon D, Graves-Lindsay TA, Munson KM, Kronenberg ZN, Vives L, Peluso P, Boitano M, Chin CS, Korlach J, Wilson RK, Eichler EE.

Genome Res. 2017 May;27(5):677-685. doi: 10.1101/gr.214007.116. Epub 2016 Nov 28.

PMID:
27895111
2.

Long-read sequence assembly of the gorilla genome.

Gordon D, Huddleston J, Chaisson MJ, Hill CM, Kronenberg ZN, Munson KM, Malig M, Raja A, Fiddes I, Hillier LW, Dunn C, Baker C, Armstrong J, Diekhans M, Paten B, Shendure J, Wilson RK, Haussler D, Chin CS, Eichler EE.

Science. 2016 Apr 1;352(6281):aae0344. doi: 10.1126/science.aae0344.

3.

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.

4.

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, Hsi-Yang Fritz M, Konkel MK, Malhotra A, St├╝tz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJ, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HY, Jasmine Mu X, 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.

5.

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.

6.

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory.

Chaisson MJ, Tesler G.

BMC Bioinformatics. 2012 Sep 19;13:238. doi: 10.1186/1471-2105-13-238.

7.

De novo fragment assembly with short mate-paired reads: Does the read length matter?

Chaisson MJ, Brinza D, Pevzner PA.

Genome Res. 2009 Feb;19(2):336-46. doi: 10.1101/gr.079053.108. Epub 2008 Dec 3.

8.

Short read fragment assembly of bacterial genomes.

Chaisson MJ, Pevzner PA.

Genome Res. 2008 Feb;18(2):324-30. Epub 2007 Dec 14.

9.

Microinversions in mammalian evolution.

Chaisson MJ, Raphael BJ, Pevzner PA.

Proc Natl Acad Sci U S A. 2006 Dec 26;103(52):19824-9. Epub 2006 Dec 22.

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