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Items: 43

1.

Sequencing 5-Hydroxymethyluracil at Single-Base Resolution.

Kawasaki F, Martínez Cuesta S, Beraldi D, Mahtey A, Hardisty RE, Carrington M, Balasubramanian S.

Angew Chem Int Ed Engl. 2018 Jun 7. doi: 10.1002/anie.201804046. [Epub ahead of print]

PMID:
29882366
2.

Psychological Resources, Personality Traits and Buddhism: A Study of Italian Young Adults.

Giannini M, Loscalzo Y, Beraldi D, Gori A.

J Relig Health. 2018 Apr 28. doi: 10.1007/s10943-018-0618-y. [Epub ahead of print]

PMID:
29705829
3.

Base resolution maps reveal the importance of 5-hydroxymethylcytosine in a human glioblastoma.

Raiber EA, Beraldi D, Martínez Cuesta S, McInroy GR, Kingsbury Z, Becq J, James T, Lopes M, Allinson K, Field S, Humphray S, Santarius T, Watts C, Bentley D, Balasubramanian S.

NPJ Genom Med. 2017 Mar 13;2:6. doi: 10.1038/s41525-017-0007-6. eCollection 2017.

4.

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.

5.

ASCIIGenome: a command line genome browser for console terminals.

Beraldi D.

Bioinformatics. 2017 May 15;33(10):1568-1569. doi: 10.1093/bioinformatics/btx007.

6.

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. Epub 2016 Sep 12.

PMID:
27618450
7.

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.

8.

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. eCollection 2016.

9.

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.

10.

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.

11.

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. eCollection 2015.

12.

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):44-49. doi: 10.1038/nsmb.2936. Epub 2014 Dec 15.

13.

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. Epub 2014 Mar 23. Erratum in: Nat Chem. Nat Chem. 2014;6(6):553.

14.

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. Epub 2013 Sep 5.

15.

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.

16.

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.

17.

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. Epub 2013 May 10.

18.

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.

19.

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.

20.

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.

21.

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. Epub 2012 Nov 6.

22.

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. Epub 2012 Sep 24.

PMID:
22998224
23.

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.

24.

Pig bone marrow-derived macrophages resemble human macrophages in their response to bacterial lipopolysaccharide.

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

J Immunol. 2012 Apr 1;188(7):3382-94. doi: 10.4049/jimmunol.1102649. Epub 2012 Mar 5.

25.

Genome-wide association mapping identifies the genetic basis of discrete and quantitative variation in sexual weaponry in a wild sheep population.

Johnston SE, McEwan JC, Pickering NK, Kijas JW, Beraldi D, Pilkington JG, Pemberton JM, Slate J.

Mol Ecol. 2011 Jun;20(12):2555-66. doi: 10.1111/j.1365-294X.2011.05076.x. Epub 2011 Mar 29.

PMID:
21651634
26.

Digital gene expression analysis of gastrointestinal helminth resistance in Scottish blackface lambs.

Pemberton JM, Beraldi D, Craig BH, Hopkins J.

Mol Ecol. 2011 Mar;20(5):910-9. doi: 10.1111/j.1365-294X.2010.04992.x. Epub 2011 Jan 12.

PMID:
21324010
27.

Mapping quantitative trait loci in a wild population using linkage and linkage disequilibrium analyses.

Hernández-Sánchez J, Chatzipli A, Beraldi D, Gratten J, Pilkington JG, Pemberton JM.

Genet Res (Camb). 2010 Aug;92(4):273-81. doi: 10.1017/S0016672310000340.

PMID:
20943008
28.

Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites.

Hunt P, Martinelli A, Modrzynska K, Borges S, Creasey A, Rodrigues L, Beraldi D, Loewe L, Fawcett R, Kumar S, Thomson M, Trivedi U, Otto TD, Pain A, Blaxter M, Cravo P.

BMC Genomics. 2010 Sep 16;11:499. doi: 10.1186/1471-2164-11-499.

29.

No evidence for warming climate theory of coat colour change in Soay sheep: a comment on Maloney et al.

Gratten J, Wilson AJ, McRae AF, Beraldi D, Visscher PM, Pemberton JM, Slate J.

Biol Lett. 2010 Oct 23;6(5):678-9; discussion 680-1. doi: 10.1098/rsbl.2010.0160. Epub 2010 Apr 7. No abstract available.

30.

A strong quantitative trait locus for wing length on chromosome 2 in a wild population of great reed warblers.

Tarka M, Akesson M, Beraldi D, Hernández-Sánchez J, Hasselquist D, Bensch S, Hansson B.

Proc Biol Sci. 2010 Aug 7;277(1692):2361-9. doi: 10.1098/rspb.2010.0033. Epub 2010 Mar 24.

31.

Horn type and horn length genes map to the same chromosomal region in Soay sheep.

Johnston SE, Beraldi D, McRae AF, Pemberton JM, Slate J.

Heredity (Edinb). 2010 Feb;104(2):196-205. doi: 10.1038/hdy.2009.109. Epub 2009 Aug 19.

32.

The genetic basis of recessive self-colour pattern in a wild sheep population.

Gratten J, Pilkington JG, Brown EA, Beraldi D, Pemberton JM, Slate J.

Heredity (Edinb). 2010 Feb;104(2):206-14. doi: 10.1038/hdy.2009.105. Epub 2009 Aug 12.

33.

Revealing the history of sheep domestication using retrovirus integrations.

Chessa B, Pereira F, Arnaud F, Amorim A, Goyache F, Mainland I, Kao RR, Pemberton JM, Beraldi D, Stear MJ, Alberti A, Pittau M, Iannuzzi L, Banabazi MH, Kazwala RR, Zhang YP, Arranz JJ, Ali BA, Wang Z, Uzun M, Dione MM, Olsaker I, Holm LE, Saarma U, Ahmad S, Marzanov N, Eythorsdottir E, Holland MJ, Ajmone-Marsan P, Bruford MW, Kantanen J, Spencer TE, Palmarini M.

Science. 2009 Apr 24;324(5926):532-6. doi: 10.1126/science.1170587.

34.

Gene mapping in the wild with SNPs: guidelines and future directions.

Slate J, Gratten J, Beraldi D, Stapley J, Hale M, Pemberton JM.

Genetica. 2009 May;136(1):97-107. doi: 10.1007/s10709-008-9317-z. Epub 2008 Sep 9. Erratum in: Genetica. 2010 Apr;138(4):467.

PMID:
18780148
35.

Phenotypic analysis of host-parasite interactions in lambs infected with Teladorsagia circumcincta.

Beraldi D, Craig BH, Bishop SC, Hopkins J, Pemberton JM.

Int J Parasitol. 2008 Nov;38(13):1567-77. doi: 10.1016/j.ijpara.2008.04.011. Epub 2008 May 24.

PMID:
18589425
36.

A localized negative genetic correlation constrains microevolution of coat color in wild sheep.

Gratten J, Wilson AJ, McRae AF, Beraldi D, Visscher PM, Pemberton JM, Slate J.

Science. 2008 Jan 18;319(5861):318-20. doi: 10.1126/science.1151182.

37.

Mapping quantitative trait Loci underlying fitness-related traits in a free-living sheep population.

Beraldi D, McRae AF, Gratten J, Slate J, Visscher PM, Pemberton JM.

Evolution. 2007 Jun;61(6):1403-16.

PMID:
17542849
38.

Compelling evidence that a single nucleotide substitution in TYRP1 is responsible for coat-colour polymorphism in a free-living population of Soay sheep.

Gratten J, Beraldi D, Lowder BV, McRae AF, Visscher PM, Pemberton JM, Slate J.

Proc Biol Sci. 2007 Mar 7;274(1610):619-26.

39.

Quantitative trait loci (QTL) mapping of resistance to strongyles and coccidia in the free-living Soay sheep (Ovis aries).

Beraldi D, McRae AF, Gratten J, Pilkington JG, Slate J, Visscher PM, Pemberton JM.

Int J Parasitol. 2007 Jan;37(1):121-9. Epub 2006 Oct 10.

PMID:
17067607
40.

Development of a linkage map and mapping of phenotypic polymorphisms in a free-living population of Soay sheep (Ovis aries).

Beraldi D, McRae AF, Gratten J, Slate J, Visscher PM, Pemberton JM.

Genetics. 2006 Jul;173(3):1521-37.

41.

Performance of marker-based relatedness estimators in natural populations of outbred vertebrates.

Csilléry K, Johnson T, Beraldi D, Clutton-Brock T, Coltman D, Hansson B, Spong G, Pemberton JM.

Genetics. 2006 Aug;173(4):2091-101. Epub 2006 Jun 18.

42.

Examination of a region showing linkage map discrepancies across sheep breeds.

McRae AF, Beraldi D.

Mamm Genome. 2006 Apr;17(4):346-53. Epub 2006 Apr 4.

PMID:
16596456
43.

Fine mapping of the parthenocarpic fruit ( pat) mutation in tomato.

Beraldi D, Picarella ME, Soressi GP, Mazzucato A.

Theor Appl Genet. 2004 Jan;108(2):209-16. Epub 2003 Oct 16.

PMID:
14564391

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