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Results: 1 to 20 of 74

1.

Enhanced reduced representation bisulfite sequencing for assessment of DNA methylation at base pair resolution.

Garrett-Bakelman FE, Sheridan CK, Kacmarczyk TJ, Ishii J, Betel D, Alonso A, Mason CE, Figueroa ME, Melnick AM.

J Vis Exp. 2015 Feb 24;(96). doi: 10.3791/52246.

2.

miR-29a maintains mouse hematopoietic stem cell self-renewal by regulating Dnmt3a.

Hu W, Dooley J, Chung SS, Chandramohan D, Cimmino L, Mukherjee S, Mason CE, de Strooper B, Liston A, Park CY.

Blood. 2015 Apr 2;125(14):2206-16. doi: 10.1182/blood-2014-06-585273. Epub 2015 Jan 29.

PMID:
25634742
3.

Comparative exomics of Phalaris cultivars under salt stress.

Haiminen N, Klaas M, Zhou Z, Utro F, Cormican P, Didion T, Jensen C, Mason CE, Barth S, Parida L.

BMC Genomics. 2014;15 Suppl 6:S18. doi: 10.1186/1471-2164-15-S6-S18. Epub 2014 Oct 17.

4.

An integrative computational approach for prioritization of genomic variants.

Dubchak I, Balasubramanian S, Wang S, Meyden C, Sulakhe D, Poliakov A, Börnigen D, Xie B, Taylor A, Ma J, Paciorkowski AR, Mirzaa GM, Dave P, Agam G, Xu J, Al-Gazali L, Mason CE, Ross ME, Maltsev N, Gilliam TC.

PLoS One. 2014 Dec 15;9(12):e114903. doi: 10.1371/journal.pone.0114903. eCollection 2014.

5.

DNA hydroxymethylation profiling reveals that WT1 mutations result in loss of TET2 function in acute myeloid leukemia.

Rampal R, Alkalin A, Madzo J, Vasanthakumar A, Pronier E, Patel J, Li Y, Ahn J, Abdel-Wahab O, Shih A, Lu C, Ward PS, Tsai JJ, Hricik T, Tosello V, Tallman JE, Zhao X, Daniels D, Dai Q, Ciminio L, Aifantis I, He C, Fuks F, Tallman MS, Ferrando A, Nimer S, Paietta E, Thompson CB, Licht JD, Mason CE, Godley LA, Melnick A, Figueroa ME, Levine RL.

Cell Rep. 2014 Dec 11;9(5):1841-55. doi: 10.1016/j.celrep.2014.11.004. Epub 2014 Dec 4.

6.

genomation: a toolkit to summarize, annotate and visualize genomic intervals.

Akalin A, Franke V, Vlahoviček K, Mason CE, Schübeler D.

Bioinformatics. 2015 Apr 1;31(7):1127-9. doi: 10.1093/bioinformatics/btu775. Epub 2014 Nov 21.

PMID:
25417204
7.

Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR).

Peng X, Thierry-Mieg J, Thierry-Mieg D, Nishida A, Pipes L, Bozinoski M, Thomas MJ, Kelly S, Weiss JM, Raveendran M, Muzny D, Gibbs RA, Rogers J, Schroth GP, Katze MG, Mason CE.

Nucleic Acids Res. 2015 Jan;43(Database issue):D737-42. doi: 10.1093/nar/gku1110. Epub 2014 Nov 11.

8.

Enabling large-scale next-generation sequence assembly with Blacklight.

Couger MB, Pipes L, Squina F, Prade R, Siepel A, Palermo R, Katze MG, Mason CE, Blood PD.

Concurr Comput. 2014 Sep 10;26(13):2157-2166.

9.

Dynamic evolution of clonal epialleles revealed by methclone.

Li S, Garrett-Bakelman F, Perl AE, Luger SM, Zhang C, To BL, Lewis ID, Brown AL, D'Andrea RJ, Ross ME, Levine R, Carroll M, Melnick A, Mason CE.

Genome Biol. 2014 Sep 27;15(9):472. doi: 10.1186/s13059-014-0472-5.

10.

Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures.

Munro SA, Lund SP, Pine PS, Binder H, Clevert DA, Conesa A, Dopazo J, Fasold M, Hochreiter S, Hong H, Jafari N, Kreil DP, Łabaj PP, Li S, Liao Y, Lin SM, Meehan J, Mason CE, Santoyo-Lopez J, Setterquist RA, Shi L, Shi W, Smyth GK, Stralis-Pavese N, Su Z, Tong W, Wang C, Wang J, Xu J, Ye Z, Yang Y, Yu Y, Salit M.

Nat Commun. 2014 Sep 25;5:5125. doi: 10.1038/ncomms6125.

PMID:
25254650
11.

No effect of caloric restriction or exercise on radiation repair capacity.

Habermann N, Makar KW, Abbenhardt C, Xiao L, Wang CY, Utsugi HK, Alfano CM, Campbell KL, Duggan C, Foster-Schubert KE, Mason CE, Imayama I, Blackburn GL, Potter JD, McTiernan A, Ulrich CM.

Med Sci Sports Exerc. 2015 May;47(5):896-904. doi: 10.1249/MSS.0000000000000480.

PMID:
25160845
12.

Detecting and correcting systematic variation in large-scale RNA sequencing data.

Li S, Łabaj PP, Zumbo P, Sykacek P, Shi W, Shi L, Phan J, Wu PY, Wang M, Wang C, Thierry-Mieg D, Thierry-Mieg J, Kreil DP, Mason CE.

Nat Biotechnol. 2014 Sep;32(9):888-95. doi: 10.1038/nbt.3000. Epub 2014 Aug 24.

13.

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study.

Li S, Tighe SW, Nicolet CM, Grove D, Levy S, Farmerie W, Viale A, Wright C, Schweitzer PA, Gao Y, Kim D, Boland J, Hicks B, Kim R, Chhangawala S, Jafari N, Raghavachari N, Gandara J, Garcia-Reyero N, Hendrickson C, Roberson D, Rosenfeld J, Smith T, Underwood JG, Wang M, Zumbo P, Baldwin DA, Grills GS, Mason CE.

Nat Biotechnol. 2014 Sep;32(9):915-25. doi: 10.1038/nbt.2972. Epub 2014 Aug 24.

14.

Cell-cycle reprogramming for PI3K inhibition overrides a relapse-specific C481S BTK mutation revealed by longitudinal functional genomics in mantle cell lymphoma.

Chiron D, Di Liberto M, Martin P, Huang X, Sharman J, Blecua P, Mathew S, Vijay P, Eng K, Ali S, Johnson A, Chang B, Ely S, Elemento O, Mason CE, Leonard JP, Chen-Kiang S.

Cancer Discov. 2014 Sep;4(9):1022-35. doi: 10.1158/2159-8290.CD-14-0098. Epub 2014 Jul 31.

15.

The pivotal regulatory landscape of RNA modifications.

Li S, Mason CE.

Annu Rev Genomics Hum Genet. 2014;15:127-50. doi: 10.1146/annurev-genom-090413-025405. Epub 2014 Jun 2.

PMID:
24898039
16.

Assessment and improvement of Indian-origin rhesus macaque and Mauritian-origin cynomolgus macaque genome annotations using deep transcriptome sequencing data.

Peng X, Pipes L, Xiong H, Green RR, Jones DC, Ruzzo WL, Schroth GP, Mason CE, Palermo RE, Katze MG.

J Med Primatol. 2014 Oct;43(5):317-28. doi: 10.1111/jmp.12125. Epub 2014 May 8.

PMID:
24810475
17.

Seasonal and geographical variation in diapause and cold hardiness of the Asian corn borer, Ostrinia furnacalis.

Xie HC, Li DS, Zhang HG, Mason CE, Wang ZY, Lu X, Cai WZ, He KL.

Insect Sci. 2014 May 6. doi: 10.1111/1744-7917.12137. [Epub ahead of print]

PMID:
24802514
18.

Bound or free: interaction of the C-terminal domain of Escherichia coli single-stranded DNA-binding protein (SSB) with the tetrameric core of SSB.

Su XC, Wang Y, Yagi H, Shishmarev D, Mason CE, Smith PJ, Vandevenne M, Dixon NE, Otting G.

Biochemistry. 2014 Apr 1;53(12):1925-34. doi: 10.1021/bi5001867. Epub 2014 Mar 18.

PMID:
24606314
19.

A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages.

Yu Y, Fuscoe JC, Zhao C, Guo C, Jia M, Qing T, Bannon DI, Lancashire L, Bao W, Du T, Luo H, Su Z, Jones WD, Moland CL, Branham WS, Qian F, Ning B, Li Y, Hong H, Guo L, Mei N, Shi T, Wang KY, Wolfinger RD, Nikolsky Y, Walker SJ, Duerksen-Hughes P, Mason CE, Tong W, Thierry-Mieg J, Thierry-Mieg D, Shi L, Wang C.

Nat Commun. 2014;5:3230. doi: 10.1038/ncomms4230.

20.

Characterizing multi-omic data in systems biology.

Mason CE, Porter SG, Smith TM.

Adv Exp Med Biol. 2014;799:15-38. doi: 10.1007/978-1-4614-8778-4_2. Review.

PMID:
24292960
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