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Expression dynamics, relationships, and transcriptional regulations of diverse transcripts in mouse spermatogenic cells.

Lin X, Han M, Cheng L, Chen J, Zhang Z, Shen T, Wang M, Wen B, Ni T, Han C.

RNA Biol. 2016 Oct 2;13(10):1011-1024. Epub 2016 Aug 25.


A Maternal System Initiating the Zygotic Developmental Program through Combinatorial Repression in the Ascidian Embryo.

Oda-Ishii I, Kubo A, Kari W, Suzuki N, Rothbächer U, Satou Y.

PLoS Genet. 2016 May 6;12(5):e1006045. doi: 10.1371/journal.pgen.1006045. eCollection 2016 May. Erratum in: PLoS Genet. 2016 Oct 14;12 (10 ):e1006392.


Conserved and Diverged Functions of the Calcineurin-Activated Prz1 Transcription Factor in Fission Yeast.

Chatfield-Reed K, Vachon L, Kwon EJ, Chua G.

Genetics. 2016 Apr;202(4):1365-75. doi: 10.1534/genetics.115.184218. Epub 2016 Feb 19.


CTCF regulates positioning of the human cystic fibrosis gene in association with a histone deacetylase.

Muck J.

Genom Data. 2014 May 10;2:82-4. doi: 10.1016/j.gdata.2014.05.002. eCollection 2014 Dec.


Choosing a suitable method for the identification of replication origins in microbial genomes.

Song C, Zhang S, Huang H.

Front Microbiol. 2015 Sep 30;6:1049. doi: 10.3389/fmicb.2015.01049. eCollection 2015. Review.


Sandcastle: software for revealing latent information in multiple experimental ChIP-chip datasets via a novel normalisation procedure.

Bennett M, Evans KE, Yu S, Teng Y, Webster RM, Powell J, Waters R, Reed SH.

Sci Rep. 2015 Aug 26;5:13395. doi: 10.1038/srep13395.


Transcriptional and Post-Transcriptional Modulation of SPI1 and SPI2 Expression by ppGpp, RpoS and DksA in Salmonella enterica sv Typhimurium.

Rice CJ, Ramachandran VK, Shearer N, Thompson A.

PLoS One. 2015 Jun 3;10(6):e0127523. doi: 10.1371/journal.pone.0127523. eCollection 2015.


MACE: model based analysis of ChIP-exo.

Wang L, Chen J, Wang C, Uusküla-Reimand L, Chen K, Medina-Rivera A, Young EJ, Zimmermann MT, Yan H, Sun Z, Zhang Y, Wu ST, Huang H, Wilson MD, Kocher JP, Li W.

Nucleic Acids Res. 2014 Nov 10;42(20):e156. doi: 10.1093/nar/gku846. Epub 2014 Sep 23.


CMT: a constrained multi-level thresholding approach for ChIP-Seq data analysis.

Rezaeian I, Rueda L.

PLoS One. 2014 Apr 15;9(4):e93873. doi: 10.1371/journal.pone.0093873. eCollection 2014.


Bacterial regulon evolution: distinct responses and roles for the identical OmpR proteins of Salmonella Typhimurium and Escherichia coli in the acid stress response.

Quinn HJ, Cameron AD, Dorman CJ.

PLoS Genet. 2014 Mar 6;10(3):e1004215. doi: 10.1371/journal.pgen.1004215. eCollection 2014 Mar.


Revealing the genetic basis of natural bacterial phenotypic divergence.

Freddolino PL, Goodarzi H, Tavazoie S.

J Bacteriol. 2014 Feb;196(4):825-39. doi: 10.1128/JB.01039-13. Epub 2013 Dec 6.


A Link between ORC-origin binding mechanisms and origin activation time revealed in budding yeast.

Hoggard T, Shor E, Müller CA, Nieduszynski CA, Fox CA.

PLoS Genet. 2013;9(9):e1003798. doi: 10.1371/journal.pgen.1003798. Epub 2013 Sep 12.


Functional characterization of fission yeast transcription factors by overexpression analysis.

Vachon L, Wood J, Kwon EJ, Laderoute A, Chatfield-Reed K, Karagiannis J, Chua G.

Genetics. 2013 Aug;194(4):873-84. doi: 10.1534/genetics.113.150870. Epub 2013 May 20.


Detection of epigenetic changes using ANOVA with spatially varying coefficients.

Guanghua X, Xinlei W, Quincey L, Nestler EJ, Xie Y.

Stat Appl Genet Mol Biol. 2013 Mar 13;12(2):189-205. doi: 10.1515/sagmb-2012-0057.


BioTile, a Perl based tool for the identification of differentially enriched regions in tiling microarray data.

Guintivano J, Arad M, Tamashiro KL, Gould TD, Kaminsky ZA.

BMC Bioinformatics. 2013 Mar 3;14:76. doi: 10.1186/1471-2105-14-76.


Deciphering the transcriptional-regulatory network of flocculation in Schizosaccharomyces pombe.

Kwon EJ, Laderoute A, Chatfield-Reed K, Vachon L, Karagiannis J, Chua G.

PLoS Genet. 2012;8(12):e1003104. doi: 10.1371/journal.pgen.1003104. Epub 2012 Dec 6.


Epigenetic change detection and pattern recognition via Bayesian hierarchical hidden Markov models.

Wang X, Zang M, Xiao G.

Stat Med. 2013 Jun 15;32(13):2292-307. doi: 10.1002/sim.5658. Epub 2012 Oct 25.


Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection.

Shibata Y, Sheffield NC, Fedrigo O, Babbitt CC, Wortham M, Tewari AK, London D, Song L, Lee BK, Iyer VR, Parker SC, Margulies EH, Wray GA, Furey TS, Crawford GE.

PLoS Genet. 2012 Jun;8(6):e1002789. doi: 10.1371/journal.pgen.1002789. Epub 2012 Jun 28.


Standardized collection of MNase-seq experiments enables unbiased dataset comparisons.

Rizzo JM, Bard JE, Buck MJ.

BMC Mol Biol. 2012 May 6;13:15. doi: 10.1186/1471-2199-13-15.


EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development.

Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR.

PLoS Genet. 2012;8(3):e1002512. doi: 10.1371/journal.pgen.1002512. Epub 2012 Mar 22.

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