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Cited In for PubMed (Select 20440878)


Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens.

Morales-Cruz A, Amrine KC, Blanco-Ulate B, Lawrence DP, Travadon R, Rolshausen PE, Baumgartner K, Cantu D.

BMC Genomics. 2015 Jun 19;16:469. doi: 10.1186/s12864-015-1624-z.


Determining the quality and complexity of next-generation sequencing data without a reference genome.

Anvar SY, Khachatryan L, Vermaat M, van Galen M, Pulyakhina I, Ariyurek Y, Kraaijeveld K, den Dunnen JT, de Knijff P, 't Hoen PA, Laros JF.

Genome Biol. 2014;15(12):555.


Reducing INDEL calling errors in whole genome and exome sequencing data.

Fang H, Wu Y, Narzisi G, O'Rawe JA, Barrón LT, Rosenbaum J, Ronemus M, Iossifov I, Schatz MC, Lyon GJ.

Genome Med. 2014 Oct 28;6(10):89. doi: 10.1186/s13073-014-0089-z. eCollection 2014.


Single haplotype assembly of the human genome from a hydatidiform mole.

Steinberg KM, Schneider VA, Graves-Lindsay TA, Fulton RS, Agarwala R, Huddleston J, Shiryev SA, Morgulis A, Surti U, Warren WC, Church DM, Eichler EE, Wilson RK.

Genome Res. 2014 Dec;24(12):2066-76. doi: 10.1101/gr.180893.114. Epub 2014 Nov 4.


In vitro, long-range sequence information for de novo genome assembly via transposase contiguity.

Adey A, Kitzman JO, Burton JN, Daza R, Kumar A, Christiansen L, Ronaghi M, Amini S, Gunderson KL, Steemers FJ, Shendure J.

Genome Res. 2014 Dec;24(12):2041-9. doi: 10.1101/gr.178319.114. Epub 2014 Oct 19.


Discovery of common sequences absent in the human reference genome using pooled samples from next generation sequencing.

Liu Y, Koyutürk M, Maxwell S, Xiang M, Veigl M, Cooper RS, Tayo BO, Li L, LaFramboise T, Wang Z, Zhu X, Chance MR.

BMC Genomics. 2014 Aug 16;15:685. doi: 10.1186/1471-2164-15-685.


Whole-genome sequencing of individuals from a founder population identifies candidate genes for asthma.

Campbell CD, Mohajeri K, Malig M, Hormozdiari F, Nelson B, Du G, Patterson KM, Eng C, Torgerson DG, Hu D, Herman C, Chong JX, Ko A, O'Roak BJ, Krumm N, Vives L, Lee C, Roth LA, Rodriguez-Cintron W, Rodriguez-Santana J, Brigino-Buenaventura E, Davis A, Meade K, LeNoir MA, Thyne S, Jackson DJ, Gern JE, Lemanske RF Jr, Shendure J, Abney M, Burchard EG, Ober C, Eichler EE.

PLoS One. 2014 Aug 12;9(8):e104396. doi: 10.1371/journal.pone.0104396. eCollection 2014.


SMaSH: a benchmarking toolkit for human genome variant calling.

Talwalkar A, Liptrap J, Newcomb J, Hartl C, Terhorst J, Curtis K, Bresler M, Song YS, Jordan MI, Patterson D.

Bioinformatics. 2014 Oct;30(19):2787-95. doi: 10.1093/bioinformatics/btu345. Epub 2014 Jun 3.


Resolving genomic disorder-associated breakpoints within segmental DNA duplications using massively parallel sequencing.

Nuttle X, Itsara A, Shendure J, Eichler EE.

Nat Protoc. 2014;9(6):1496-513. doi: 10.1038/nprot.2014.096. Epub 2014 May 29.


The genetics of microdeletion and microduplication syndromes: an update.

Watson CT, Marques-Bonet T, Sharp AJ, Mefford HC.

Annu Rev Genomics Hum Genet. 2014;15:215-44. doi: 10.1146/annurev-genom-091212-153408. Epub 2014 Apr 16. Review.


Low frequency variants, collapsed based on biological knowledge, uncover complexity of population stratification in 1000 genomes project data.

Moore CB, Wallace JR, Wolfe DJ, Frase AT, Pendergrass SA, Weiss KM, Ritchie MD.

PLoS Genet. 2013;9(12):e1003959. doi: 10.1371/journal.pgen.1003959. Epub 2013 Dec 26.


Properties and rates of germline mutations in humans.

Campbell CD, Eichler EE.

Trends Genet. 2013 Oct;29(10):575-84. doi: 10.1016/j.tig.2013.04.005. Epub 2013 May 16. Review.


Improving mammalian genome scaffolding using large insert mate-pair next-generation sequencing.

van Heesch S, Kloosterman WP, Lansu N, Ruzius FP, Levandowsky E, Lee CC, Zhou S, Goldstein S, Schwartz DC, Harkins TT, Guryev V, Cuppen E.

BMC Genomics. 2013 Apr 16;14:257. doi: 10.1186/1471-2164-14-257.


Complete haplotype sequence of the human immunoglobulin heavy-chain variable, diversity, and joining genes and characterization of allelic and copy-number variation.

Watson CT, Steinberg KM, Huddleston J, Warren RL, Malig M, Schein J, Willsey AJ, Joy JB, Scott JK, Graves TA, Wilson RK, Holt RA, Eichler EE, Breden F.

Am J Hum Genet. 2013 Apr 4;92(4):530-46. doi: 10.1016/j.ajhg.2013.03.004. Epub 2013 Mar 28.


Using population admixture to help complete maps of the human genome.

Genovese G, Handsaker RE, Li H, Altemose N, Lindgren AM, Chambert K, Pasaniuc B, Price AL, Reich D, Morton CC, Pollak MR, Wilson JG, McCarroll SA.

Nat Genet. 2013 Apr;45(4):406-14, 414e1-2. doi: 10.1038/ng.2565. Epub 2013 Feb 24.


Incorporating the human gene annotations in different databases significantly improved transcriptomic and genetic analyses.

Chen G, Wang C, Shi L, Qu X, Chen J, Yang J, Shi C, Chen L, Zhou P, Ning B, Tong W, Shi T.

RNA. 2013 Apr;19(4):479-89. doi: 10.1261/rna.037473.112. Epub 2013 Feb 19.


AZFc deletions and spermatogenic failure: a population-based survey of 20,000 Y chromosomes.

Rozen SG, Marszalek JD, Irenze K, Skaletsky H, Brown LG, Oates RD, Silber SJ, Ardlie K, Page DC.

Am J Hum Genet. 2012 Nov 2;91(5):890-6. doi: 10.1016/j.ajhg.2012.09.003. Epub 2012 Oct 25.


Limitations of the human reference genome for personalized genomics.

Rosenfeld JA, Mason CE, Smith TM.

PLoS One. 2012;7(7):e40294. doi: 10.1371/journal.pone.0040294. Epub 2012 Jul 11.


Protein genes in repetitive sequence-antifreeze glycoproteins in Atlantic cod genome.

Zhuang X, Yang C, Fevolden SE, Cheng CH.

BMC Genomics. 2012 Jul 2;13:293. doi: 10.1186/1471-2164-13-293.


Dissect: detection and characterization of novel structural alterations in transcribed sequences.

Yorukoglu D, Hach F, Swanson L, Collins CC, Birol I, Sahinalp SC.

Bioinformatics. 2012 Jun 15;28(12):i179-87. doi: 10.1093/bioinformatics/bts214.

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