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Items: 1 to 20 of 191

1.

Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing.

Heap GA, Yang JH, Downes K, Healy BC, Hunt KA, Bockett N, Franke L, Dubois PC, Mein CA, Dobson RJ, Albert TJ, Rodesch MJ, Clayton DG, Todd JA, van Heel DA, Plagnol V.

Hum Mol Genet. 2010 Jan 1;19(1):122-34. doi: 10.1093/hmg/ddp473.

2.

Removing reference mapping biases using limited or no genotype data identifies allelic differences in protein binding at disease-associated loci.

Buchkovich ML, Eklund K, Duan Q, Li Y, Mohlke KL, Furey TS.

BMC Med Genomics. 2015 Jul 26;8:43. doi: 10.1186/s12920-015-0117-x.

3.

Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data.

Wood DL, Nones K, Steptoe A, Christ A, Harliwong I, Newell F, Bruxner TJ, Miller D, Cloonan N, Grimmond SM.

PLoS One. 2015 May 12;10(5):e0126911. doi: 10.1371/journal.pone.0126911. eCollection 2015.

4.

Detection of allelic imbalance in gene expression using pyrosequencing.

Wang H, Elbein SC.

Methods Mol Biol. 2007;373:157-76.

PMID:
17185765
5.

Analyzing allele specific RNA expression using mixture models.

Lu R, Smith RM, Seweryn M, Wang D, Hartmann K, Webb A, Sadee W, Rempala GA.

BMC Genomics. 2015 Aug 1;16:566. doi: 10.1186/s12864-015-1749-0.

6.
7.

Powerful identification of cis-regulatory SNPs in human primary monocytes using allele-specific gene expression.

Almlöf JC, Lundmark P, Lundmark A, Ge B, Maouche S, Göring HH, Liljedahl U, Enström C, Brocheton J, Proust C, Godefroy T, Sambrook JG, Jolley J, Crisp-Hihn A, Foad N, Lloyd-Jones H, Stephens J, Gwilliam R, Rice CM, Hengstenberg C, Samani NJ, Erdmann J, Schunkert H, Pastinen T, Deloukas P, Goodall AH, Ouwehand WH, Cambien F, Syvänen AC.

PLoS One. 2012;7(12):e52260. doi: 10.1371/journal.pone.0052260. Epub 2012 Dec 26.

8.

Single Nucleotide Polymorphism Discovery in Bovine Pituitary Gland Using RNA-Seq Technology.

Pareek CS, Smoczyński R, Kadarmideen HN, Dziuba P, Błaszczyk P, Sikora M, Walendzik P, Grzybowski T, Pierzchała M, Horbańczuk J, Szostak A, Ogluszka M, Zwierzchowski L, Czarnik U, Fraser L, Sobiech P, Wąsowicz K, Gelfand B, Feng Y, Kumar D.

PLoS One. 2016 Sep 8;11(9):e0161370. doi: 10.1371/journal.pone.0161370. eCollection 2016.

9.

Comparing computational methods for identification of allele-specific expression based on next generation sequencing data.

Liu Z, Yang J, Xu H, Li C, Wang Z, Li Y, Dong X, Li Y.

Genet Epidemiol. 2014 Nov;38(7):591-8. doi: 10.1002/gepi.21846. Epub 2014 Sep 2.

PMID:
25183311
10.

Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis.

Baranzini SE, Mudge J, van Velkinburgh JC, Khankhanian P, Khrebtukova I, Miller NA, Zhang L, Farmer AD, Bell CJ, Kim RW, May GD, Woodward JE, Caillier SJ, McElroy JP, Gomez R, Pando MJ, Clendenen LE, Ganusova EE, Schilkey FD, Ramaraj T, Khan OA, Huntley JJ, Luo S, Kwok PY, Wu TD, Schroth GP, Oksenberg JR, Hauser SL, Kingsmore SF.

Nature. 2010 Apr 29;464(7293):1351-6. doi: 10.1038/nature08990.

11.

Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array.

Liu S, Zhou Z, Lu J, Sun F, Wang S, Liu H, Jiang Y, Kucuktas H, Kaltenboeck L, Peatman E, Liu Z.

BMC Genomics. 2011 Jan 21;12:53. doi: 10.1186/1471-2164-12-53.

12.

Transcriptome genetics using second generation sequencing in a Caucasian population.

Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, Nisbett J, Guigo R, Dermitzakis ET.

Nature. 2010 Apr 1;464(7289):773-7. doi: 10.1038/nature08903. Epub 2010 Mar 10.

13.

High-throughput RNA-seq for allelic or locus-specific expression analysis in Arabidopsis-related species, hybrids, and allotetraploids.

Ng DW, Shi X, Nah G, Chen ZJ.

Methods Mol Biol. 2014;1112:33-48. doi: 10.1007/978-1-62703-773-0_3.

PMID:
24478006
14.

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.

Degner JF, Marioni JC, Pai AA, Pickrell JK, Nkadori E, Gilad Y, Pritchard JK.

Bioinformatics. 2009 Dec 15;25(24):3207-12. doi: 10.1093/bioinformatics/btp579. Epub 2009 Oct 6.

15.

Accurate detection and genotyping of SNPs utilizing population sequencing data.

Bansal V, Harismendy O, Tewhey R, Murray SS, Schork NJ, Topol EJ, Frazer KA.

Genome Res. 2010 Apr;20(4):537-45. doi: 10.1101/gr.100040.109. Epub 2010 Feb 11.

16.

Extensive variation between tissues in allele specific expression in an outbred mammal.

Chamberlain AJ, Vander Jagt CJ, Hayes BJ, Khansefid M, Marett LC, Millen CA, Nguyen TT, Goddard ME.

BMC Genomics. 2015 Nov 23;16:993. doi: 10.1186/s12864-015-2174-0.

17.

Next-generation DNA sequencing-based assay for measuring allelic expression imbalance (AEI) of candidate neuropsychiatric disorder genes in human brain.

Xu X, Wang H, Zhu M, Sun Y, Tao Y, He Q, Wang J, Chen L, Saffen D.

BMC Genomics. 2011 Oct 20;12:518. doi: 10.1186/1471-2164-12-518.

18.

Identification of imprinted loci by transcriptome sequencing.

Babak T.

Methods Mol Biol. 2012;925:79-88. doi: 10.1007/978-1-62703-011-3_6.

PMID:
22907492
19.

Allelic expression imbalance of the schizophrenia susceptibility gene CHI3L1: evidence of cis-acting variation and tissue specific regulation.

Hill MJ, Kenny E, Roche S, Morris DW, Corvin A, Hawi Z, Gill M, Anney RJ.

Psychiatr Genet. 2011 Dec;21(6):281-6. doi: 10.1097/YPG.0b013e328348045b.

PMID:
21642896
20.

dsPIG: a tool to predict imprinted genes from the deep sequencing of whole transcriptomes.

Li H, Su X, Gallegos J, Lu Y, Ji Y, Molldrem JJ, Liang S.

BMC Bioinformatics. 2012 Oct 19;13:271. doi: 10.1186/1471-2105-13-271.

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