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Items: 10

1.

Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation.

Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE, Haussler D, Stanke M, Paten B.

Genome Res. 2018 Jul;28(7):1029-1038. doi: 10.1101/gr.233460.117. Epub 2018 Jun 8.

2.

High-resolution comparative analysis of great ape genomes.

Kronenberg ZN, Fiddes IT, Gordon D, Murali S, Cantsilieris S, Meyerson OS, Underwood JG, Nelson BJ, Chaisson MJP, Dougherty ML, Munson KM, Hastie AR, Diekhans M, Hormozdiari F, Lorusso N, Hoekzema K, Qiu R, Clark K, Raja A, Welch AE, Sorensen M, Baker C, Fulton RS, Armstrong J, Graves-Lindsay TA, Denli AM, Hoppe ER, Hsieh P, Hill CM, Pang AWC, Lee J, Lam ET, Dutcher SK, Gage FH, Warren WC, Shendure J, Haussler D, Schneider VA, Cao H, Ventura M, Wilson RK, Paten B, Pollen A, Eichler EE.

Science. 2018 Jun 8;360(6393). pii: eaar6343. doi: 10.1126/science.aar6343.

3.

Corrigendum: 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. 2018 Jan;28(1):144. doi: 10.1101/gr.233007.117. No abstract available.

4.

Genomic Patterns of De Novo Mutation in Simplex Autism.

Turner TN, Coe BP, Dickel DE, Hoekzema K, Nelson BJ, Zody MC, Kronenberg ZN, Hormozdiari F, Raja A, Pennacchio LA, Darnell RB, Eichler EE.

Cell. 2017 Oct 19;171(3):710-722.e12. doi: 10.1016/j.cell.2017.08.047. Epub 2017 Sep 28.

5.

Emergence of a Viral RNA Polymerase Variant during Gene Copy Number Amplification Promotes Rapid Evolution of Vaccinia Virus.

Cone KR, Kronenberg ZN, Yandell M, Elde NC.

J Virol. 2017 Jan 31;91(4). pii: e01428-16. doi: 10.1128/JVI.01428-16. Print 2017 Feb 15.

6.

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. Erratum in: Genome Res. 2018 Jan;28(1):144.

7.

De novo genic mutations among a Chinese autism spectrum disorder cohort.

Wang T, Guo H, Xiong B, Stessman HA, Wu H, Coe BP, Turner TN, Liu Y, Zhao W, Hoekzema K, Vives L, Xia L, Tang M, Ou J, Chen B, Shen Y, Xun G, Long M, Lin J, Kronenberg ZN, Peng Y, Bai T, Li H, Ke X, Hu Z, Zhao J, Zou X, Xia K, Eichler EE.

Nat Commun. 2016 Nov 8;7:13316. doi: 10.1038/ncomms13316.

8.

Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region.

Mohajeri K, Cantsilieris S, Huddleston J, Nelson BJ, Coe BP, Campbell CD, Baker C, Harshman L, Munson KM, Kronenberg ZN, Kremitzki M, Raja A, Catacchio CR, Graves TA, Wilson RK, Ventura M, Eichler EE.

Genome Res. 2016 Nov;26(11):1453-1467. Epub 2016 Oct 7.

9.

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.

10.

Wham: Identifying Structural Variants of Biological Consequence.

Kronenberg ZN, Osborne EJ, Cone KR, Kennedy BJ, Domyan ET, Shapiro MD, Elde NC, Yandell M.

PLoS Comput Biol. 2015 Dec 1;11(12):e1004572. doi: 10.1371/journal.pcbi.1004572. eCollection 2015 Dec.

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