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Items: 1 to 20 of 40

1.

Genome-wide mapping of 5-hydroxymethyluracil in the eukaryote parasite Leishmania.

Kawasaki F, Beraldi D, Hardisty RE, McInroy GR, van Delft P, Balasubramanian S.

Genome Biol. 2017 Jan 30;18(1):23. doi: 10.1186/s13059-017-1150-1.

2.

ASCIIGenome: A command line genome browser for console terminals.

Beraldi D.

Bioinformatics. 2017 Jan 24. pii: btx007. doi: 10.1093/bioinformatics/btx007. [Epub ahead of print]

PMID:
28119307
3.

G-quadruplex structures mark human regulatory chromatin.

Hänsel-Hertsch R, Beraldi D, Lensing SV, Marsico G, Zyner K, Parry A, Di Antonio M, Pike J, Kimura H, Narita M, Tannahill D, Balasubramanian S.

Nat Genet. 2016 Oct;48(10):1267-72. doi: 10.1038/ng.3662.

PMID:
27618450
4.

In vivo genome-wide profiling reveals a tissue-specific role for 5-formylcytosine.

Iurlaro M, McInroy GR, Burgess HE, Dean W, Raiber EA, Bachman M, Beraldi D, Balasubramanian S, Reik W.

Genome Biol. 2016 Jun 29;17(1):141. doi: 10.1186/s13059-016-1001-5.

5.

Enhanced Methylation Analysis by Recovery of Unsequenceable Fragments.

McInroy GR, Beraldi D, Raiber EA, Modrzynska K, van Delft P, Billker O, Balasubramanian S.

PLoS One. 2016 Mar 31;11(3):e0152322. doi: 10.1371/journal.pone.0152322.

6.

Identification and annotation of conserved promoters and macrophage-expressed genes in the pig genome.

Robert C, Kapetanovic R, Beraldi D, Watson M, Archibald AL, Hume DA.

BMC Genomics. 2015 Nov 18;16:970. doi: 10.1186/s12864-015-2111-2.

7.

FOXM1 binds directly to non-consensus sequences in the human genome.

Sanders DA, Gormally MV, Marsico G, Beraldi D, Tannahill D, Balasubramanian S.

Genome Biol. 2015 Jun 23;16:130. doi: 10.1186/s13059-015-0696-z.

8.

Accurate measurement of 5-methylcytosine and 5-hydroxymethylcytosine in human cerebellum DNA by oxidative bisulfite on an array (OxBS-array).

Field SF, Beraldi D, Bachman M, Stewart SK, Beck S, Balasubramanian S.

PLoS One. 2015 Feb 23;10(2):e0118202. doi: 10.1371/journal.pone.0118202.

9.

5-Formylcytosine alters the structure of the DNA double helix.

Raiber EA, Murat P, Chirgadze DY, Beraldi D, Luisi BF, Balasubramanian S.

Nat Struct Mol Biol. 2015 Jan;22(1):44-9. doi: 10.1038/nsmb.2936.

10.

Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution.

Booth MJ, Marsico G, Bachman M, Beraldi D, Balasubramanian S.

Nat Chem. 2014 May;6(5):435-40. doi: 10.1038/nchem.1893. Erratum in: Nat Chem. Nat Chem. 2014;6(6):553.

11.

Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine.

Booth MJ, Ost TW, Beraldi D, Bell NM, Branco MR, Reik W, Balasubramanian S.

Nat Protoc. 2013 Oct;8(10):1841-51. doi: 10.1038/nprot.2013.115.

12.

The impact of breed and tissue compartment on the response of pig macrophages to lipopolysaccharide.

Kapetanovic R, Fairbairn L, Downing A, Beraldi D, Sester DP, Freeman TC, Tuggle CK, Archibald AL, Hume DA.

BMC Genomics. 2013 Aug 28;14:581. doi: 10.1186/1471-2164-14-581.

13.

Structural and functional annotation of the porcine immunome.

Dawson HD, Loveland JE, Pascal G, Gilbert JG, Uenishi H, Mann KM, Sang Y, Zhang J, Carvalho-Silva D, Hunt T, Hardy M, Hu Z, Zhao SH, Anselmo A, Shinkai H, Chen C, Badaoui B, Berman D, Amid C, Kay M, Lloyd D, Snow C, Morozumi T, Cheng RP, Bystrom M, Kapetanovic R, Schwartz JC, Kataria R, Astley M, Fritz E, Steward C, Thomas M, Wilming L, Toki D, Archibald AL, Bed'Hom B, Beraldi D, Huang TH, Ait-Ali T, Blecha F, Botti S, Freeman TC, Giuffra E, Hume DA, Lunney JK, Murtaugh MP, Reecy JM, Harrow JL, Rogel-Gaillard C, Tuggle CK.

BMC Genomics. 2013 May 15;14:332. doi: 10.1186/1471-2164-14-332.

14.

Comparative analysis of monocyte subsets in the pig.

Fairbairn L, Kapetanovic R, Beraldi D, Sester DP, Tuggle CK, Archibald AL, Hume DA.

J Immunol. 2013 Jun 15;190(12):6389-96. doi: 10.4049/jimmunol.1300365.

15.

G-quadruplex structures are stable and detectable in human genomic DNA.

Lam EY, Beraldi D, Tannahill D, Balasubramanian S.

Nat Commun. 2013;4:1796. doi: 10.1038/ncomms2792.

16.

Genome-wide mapping of FOXM1 binding reveals co-binding with estrogen receptor alpha in breast cancer cells.

Sanders DA, Ross-Innes CS, Beraldi D, Carroll JS, Balasubramanian S.

Genome Biol. 2013 Jan 24;14(1):R6. doi: 10.1186/gb-2013-14-1-r6.

17.

A gene expression atlas of the domestic pig.

Freeman TC, Ivens A, Baillie JK, Beraldi D, Barnett MW, Dorward D, Downing A, Fairbairn L, Kapetanovic R, Raza S, Tomoiu A, Alberio R, Wu C, Su AI, Summers KM, Tuggle CK, Archibald AL, Hume DA.

BMC Biol. 2012 Nov 15;10:90. doi: 10.1186/1741-7007-10-90.

18.

Prediction of altered 3'- UTR miRNA-binding sites from RNA-Seq data: the swine leukocyte antigen complex (SLA) as a model region.

Endale Ahanda ML, Fritz ER, Estellé J, Hu ZL, Madsen O, Groenen MA, Beraldi D, Kapetanovic R, Hume DA, Rowland RR, Lunney JK, Rogel-Gaillard C, Reecy JM, Giuffra E.

PLoS One. 2012;7(11):e48607. doi: 10.1371/journal.pone.0048607.

19.

Detecting genes for variation in parasite burden and immunological traits in a wild population: testing the candidate gene approach.

Brown EA, Pilkington JG, Nussey DH, Watt KA, Hayward AD, Tucker R, Graham AL, Paterson S, Beraldi D, Pemberton JM, Slate J.

Mol Ecol. 2013 Feb;22(3):757-73. doi: 10.1111/j.1365-294X.2012.05757.x.

PMID:
22998224
20.

Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase.

Raiber EA, Beraldi D, Ficz G, Burgess HE, Branco MR, Murat P, Oxley D, Booth MJ, Reik W, Balasubramanian S.

Genome Biol. 2012 Aug 17;13(8):R69. doi: 10.1186/gb-2012-13-8-r69.

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