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Items: 1 to 20 of 101


Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2.

Zhou B, Ho SS, Greer SU, Spies N, Bell JM, Zhang X, Zhu X, Arthur JG, Byeon S, Pattni R, Saha I, Huang Y, Song G, Perrin D, Wong WH, Ji HP, Abyzov A, Urban AE.

Nucleic Acids Res. 2019 May 7;47(8):3846-3861. doi: 10.1093/nar/gkz169.


Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562.

Zhou B, Ho SS, Greer SU, Zhu X, Bell JM, Arthur JG, Spies N, Zhang X, Byeon S, Pattni R, Ben-Efraim N, Haney MS, Haraksingh RR, Song G, Ji HP, Perrin D, Wong WH, Abyzov A, Urban AE.

Genome Res. 2019 Mar;29(3):472-484. doi: 10.1101/gr.234948.118. Epub 2019 Feb 8.


The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line.

Adey A, Burton JN, Kitzman JO, Hiatt JB, Lewis AP, Martin BK, Qiu R, Lee C, Shendure J.

Nature. 2013 Aug 8;500(7461):207-11. doi: 10.1038/nature12064.


Allele-Specific Quantification of Structural Variations in Cancer Genomes.

Li Y, Zhou S, Schwartz DC, Ma J.

Cell Syst. 2016 Jul;3(1):21-34. doi: 10.1016/j.cels.2016.05.007. Epub 2016 Jul 21.


SvABA: genome-wide detection of structural variants and indels by local assembly.

Wala JA, Bandopadhayay P, Greenwald NF, O'Rourke R, Sharpe T, Stewart C, Schumacher S, Li Y, Weischenfeldt J, Yao X, Nusbaum C, Campbell P, Getz G, Meyerson M, Zhang CZ, Imielinski M, Beroukhim R.

Genome Res. 2018 Apr;28(4):581-591. doi: 10.1101/gr.221028.117. Epub 2018 Mar 13.


Chromosome-scale mega-haplotypes enable digital karyotyping of cancer aneuploidy.

Bell JM, Lau BT, Greer SU, Wood-Bouwens C, Xia LC, Connolly ID, Gephart MH, Ji HP.

Nucleic Acids Res. 2017 Nov 2;45(19):e162. doi: 10.1093/nar/gkx712.


Picky comprehensively detects high-resolution structural variants in nanopore long reads.

Gong L, Wong CH, Cheng WC, Tjong H, Menghi F, Ngan CY, Liu ET, Wei CL.

Nat Methods. 2018 Jun;15(6):455-460. doi: 10.1038/s41592-018-0002-6. Epub 2018 Apr 30.


Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects.

Gonçalves E, Behan FM, Louzada S, Arnol D, Stronach EA, Yang F, Yusa K, Stegle O, Iorio F, Garnett MJ.

Genome Biol. 2019 Feb 5;20(1):27. doi: 10.1186/s13059-019-1637-z.


Toward Recovering Allele-specific Cancer Genome Graphs.

Rajaraman A, Ma J.

J Comput Biol. 2018 Jul;25(7):624-636. doi: 10.1089/cmb.2018.0022. Epub 2018 Apr 16.


Characteristics of de novo structural changes in the human genome.

Kloosterman WP, Francioli LC, Hormozdiari F, Marschall T, Hehir-Kwa JY, Abdellaoui A, Lameijer EW, Moed MH, Koval V, Renkens I, van Roosmalen MJ, Arp P, Karssen LC, Coe BP, Handsaker RE, Suchiman ED, Cuppen E, Thung DT, McVey M, Wendl MC; Genome of Netherlands Consortium, Uitterlinden A, van Duijn CM, Swertz MA, Wijmenga C, van Ommen GB, Slagboom PE, Boomsma DI, Schönhuth A, Eichler EE, de Bakker PI, Ye K, Guryev V.

Genome Res. 2015 Jun;25(6):792-801. doi: 10.1101/gr.185041.114. Epub 2015 Apr 16.


Next generation mapping reveals novel large genomic rearrangements in prostate cancer.

Jaratlerdsiri W, Chan EKF, Petersen DC, Yang C, Croucher PI, Bornman MSR, Sheth P, Hayes VM.

Oncotarget. 2017 Apr 4;8(14):23588-23602. doi: 10.18632/oncotarget.15802.


A high-quality human reference panel reveals the complexity and distribution of genomic structural variants.

Hehir-Kwa JY, Marschall T, Kloosterman WP, Francioli LC, Baaijens JA, Dijkstra LJ, Abdellaoui A, Koval V, Thung DT, Wardenaar R, Renkens I, Coe BP, Deelen P, de Ligt J, Lameijer EW, van Dijk F, Hormozdiari F; Genome of the Netherlands Consortium, Uitterlinden AG, van Duijn CM, Eichler EE, de Bakker PI, Swertz MA, Wijmenga C, van Ommen GB, Slagboom PE, Boomsma DI, Schönhuth A, Ye K, Guryev V.

Nat Commun. 2016 Oct 6;7:12989. doi: 10.1038/ncomms12989.


Linked read sequencing resolves complex genomic rearrangements in gastric cancer metastases.

Greer SU, Nadauld LD, Lau BT, Chen J, Wood-Bouwens C, Ford JM, Kuo CJ, Ji HP.

Genome Med. 2017 Jun 19;9(1):57. doi: 10.1186/s13073-017-0447-8.


DELLY: structural variant discovery by integrated paired-end and split-read analysis.

Rausch T, Zichner T, Schlattl A, Stütz AM, Benes V, Korbel JO.

Bioinformatics. 2012 Sep 15;28(18):i333-i339. doi: 10.1093/bioinformatics/bts378.


Low incidence of SNVs and indels in trio genomes of Cas9-mediated multiplex edited sheep.

Wang X, Liu J, Niu Y, Li Y, Zhou S, Li C, Ma B, Kou Q, Petersen B, Sonstegard T, Huang X, Jiang Y, Chen Y.

BMC Genomics. 2018 May 25;19(1):397. doi: 10.1186/s12864-018-4712-z.


Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology.

Cao H, Hastie AR, Cao D, Lam ET, Sun Y, Huang H, Liu X, Lin L, Andrews W, Chan S, Huang S, Tong X, Requa M, Anantharaman T, Krogh A, Yang H, Cao H, Xu X.

Gigascience. 2014 Dec 30;3(1):34. doi: 10.1186/2047-217X-3-34. eCollection 2014.


A common copy-number breakpoint of ERBB2 amplification in breast cancer colocalizes with a complex block of segmental duplications.

Marotta M, Chen X, Inoshita A, Stephens R, Budd GT, Crowe JP, Lyons J, Kondratova A, Tubbs R, Tanaka H.

Breast Cancer Res. 2012 Nov 26;14(6):R150. doi: 10.1186/bcr3362.


The complex architecture and epigenomic impact of plant T-DNA insertions.

Jupe F, Rivkin AC, Michael TP, Zander M, Motley ST, Sandoval JP, Slotkin RK, Chen H, Castanon R, Nery JR, Ecker JR.

PLoS Genet. 2019 Jan 18;15(1):e1007819. doi: 10.1371/journal.pgen.1007819. eCollection 2019 Jan.


Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA).

Richard Albert J, Koike T, Younesy H, Thompson R, Bogutz AB, Karimi MM, Lorincz MC.

BMC Genomics. 2018 Jun 15;19(1):463. doi: 10.1186/s12864-018-4835-2.


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.


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