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Results: 1 to 20 of 28

1.

Dynamics of gene silencing during X inactivation using allele-specific RNA-seq.

Marks H, Kerstens HH, Barakat TS, Splinter E, Dirks RA, van Mierlo G, Joshi O, Wang SY, Babak T, Albers CA, Kalkan T, Smith A, Jouneau A, de Laat W, Gribnau J, Stunnenberg HG.

Genome Biol. 2015 Aug 3;16(1):149. doi: 10.1186/s13059-015-0698-x.

2.

Genetic conflict reflected in tissue-specific maps of genomic imprinting in human and mouse.

Babak T, DeVeale B, Tsang EK, Zhou Y, Li X, Smith KS, Kukurba KR, Zhang R, Li JB, van der Kooy D, Montgomery SB, Fraser HB.

Nat Genet. 2015 May;47(5):544-9. doi: 10.1038/ng.3274. Epub 2015 Apr 13.

PMID:
25848752
3.

Oct4 is required ~E7.5 for proliferation in the primitive streak.

DeVeale B, Brokhman I, Mohseni P, Babak T, Yoon C, Lin A, Onishi K, Tomilin A, Pevny L, Zandstra PW, Nagy A, van der Kooy D.

PLoS Genet. 2013 Nov;9(11):e1003957. doi: 10.1371/journal.pgen.1003957. Epub 2013 Nov 14.

4.

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
5.

Global analysis of the evolution and mechanism of echinocandin resistance in Candida glabrata.

Singh-Babak SD, Babak T, Diezmann S, Hill JA, Xie JL, Chen YL, Poutanen SM, Rennie RP, Heitman J, Cowen LE.

PLoS Pathog. 2012;8(5):e1002718. doi: 10.1371/journal.ppat.1002718. Epub 2012 May 17.

6.

Critical evaluation of imprinted gene expression by RNA-Seq: a new perspective.

DeVeale B, van der Kooy D, Babak T.

PLoS Genet. 2012;8(3):e1002600. doi: 10.1371/journal.pgen.1002600. Epub 2012 Mar 29.

7.

A quantitative atlas of polyadenylation in five mammals.

Derti A, Garrett-Engele P, Macisaac KD, Stevens RC, Sriram S, Chen R, Rohl CA, Johnson JM, Babak T.

Genome Res. 2012 Jun;22(6):1173-83. doi: 10.1101/gr.132563.111. Epub 2012 Mar 27.

8.

Systematic detection of polygenic cis-regulatory evolution.

Fraser HB, Babak T, Tsang J, Zhou Y, Zhang B, Mehrabian M, Schadt EE.

PLoS Genet. 2011 Mar;7(3):e1002023. doi: 10.1371/journal.pgen.1002023. Epub 2011 Mar 31.

9.

NSR-seq transcriptional profiling enables identification of a gene signature of Plasmodium falciparum parasites infecting children.

Vignali M, Armour CD, Chen J, Morrison R, Castle JC, Biery MC, Bouzek H, Moon W, Babak T, Fried M, Raymond CK, Duffy PE.

J Clin Invest. 2011 Mar;121(3):1119-29. doi: 10.1172/JCI43457. Epub 2011 Feb 7.

10.

Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation.

Babak T, Garrett-Engele P, Armour CD, Raymond CK, Keller MP, Chen R, Rohl CA, Johnson JM, Attie AD, Fraser HB, Schadt EE.

BMC Genomics. 2010 Aug 13;11:473. doi: 10.1186/1471-2164-11-473.

11.

Global survey of escape from X inactivation by RNA-sequencing in mouse.

Yang F, Babak T, Shendure J, Disteche CM.

Genome Res. 2010 May;20(5):614-22. doi: 10.1101/gr.103200.109. Epub 2010 Apr 2.

12.

A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300.

Khanna M, Van Bakel H, Tang X, Calarco JA, Babak T, Guo G, Emili A, Greenblatt JF, Hughes TR, Krogan NJ, Blencowe BJ.

RNA. 2009 Dec;15(12):2174-85. doi: 10.1261/rna.1790509. Epub 2009 Sep 29.

13.

Digital transcriptome profiling using selective hexamer priming for cDNA synthesis.

Armour CD, Castle JC, Chen R, Babak T, Loerch P, Jackson S, Shah JK, Dey J, Rohl CA, Johnson JM, Raymond CK.

Nat Methods. 2009 Sep;6(9):647-9. doi: 10.1038/nmeth.1360. Epub 2009 Aug 9.

PMID:
19668204
14.

Conservation of core gene expression in vertebrate tissues.

Chan ET, Quon GT, Chua G, Babak T, Trochesset M, Zirngibl RA, Aubin J, Ratcliffe MJ, Wilde A, Brudno M, Morris QD, Hughes TR.

J Biol. 2009;8(3):33. doi: 10.1186/jbiol130. Epub 2009 Apr 16.

15.

Prediction and verification of mouse tRNA gene families.

Coughlin DJ, Babak T, Nihranz C, Hughes TR, Engelke DR.

RNA Biol. 2009 Apr-Jun;6(2):195-202. Epub 2009 May 1.

16.

Global survey of genomic imprinting by transcriptome sequencing.

Babak T, Deveale B, Armour C, Raymond C, Cleary MA, van der Kooy D, Johnson JM, Lim LP.

Curr Biol. 2008 Nov 25;18(22):1735-41. doi: 10.1016/j.cub.2008.09.044.

17.

miRNA and piRNA localization in the male mammalian meiotic nucleus.

Marcon E, Babak T, Chua G, Hughes T, Moens PB.

Chromosome Res. 2008;16(2):243-60. doi: 10.1007/s10577-007-1190-6. Epub 2008 Jan 22.

PMID:
18204908
18.

Using expression profiling data to identify human microRNA targets.

Huang JC, Babak T, Corson TW, Chua G, Khan S, Gallie BL, Hughes TR, Blencowe BJ, Frey BJ, Morris QD.

Nat Methods. 2007 Dec;4(12):1045-9. Epub 2007 Nov 18.

PMID:
18026111
19.

Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function.

Lécuyer E, Yoshida H, Parthasarathy N, Alm C, Babak T, Cerovina T, Hughes TR, Tomancak P, Krause HM.

Cell. 2007 Oct 5;131(1):174-87.

20.

Functional coordination of alternative splicing in the mammalian central nervous system.

Fagnani M, Barash Y, Ip JY, Misquitta C, Pan Q, Saltzman AL, Shai O, Lee L, Rozenhek A, Mohammad N, Willaime-Morawek S, Babak T, Zhang W, Hughes TR, van der Kooy D, Frey BJ, Blencowe BJ.

Genome Biol. 2007;8(6):R108.

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