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Items: 27

1.

A validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseases.

Gawel DR, Serra-Musach J, Lilja S, Aagesen J, Arenas A, Asking B, Bengnér M, Björkander J, Biggs S, Ernerudh J, Hjortswang H, Karlsson JE, Köpsen M, Lee EJ, Lentini A, Li X, Magnusson M, Martínez-Enguita D, Matussek A, Nestor CE, Schäfer S, Seifert O, Sonmez C, Stjernman H, Tjärnberg A, Wu S, Åkesson K, Shalek AK, Stenmarker M, Zhang H, Gustafsson M, Benson M.

Genome Med. 2019 Jul 30;11(1):47. doi: 10.1186/s13073-019-0657-3.

2.

TCF/LEF dependent and independent transcriptional regulation of Wnt/β-catenin target genes.

Doumpas N, Lampart F, Robinson MD, Lentini A, Nestor CE, Cantù C, Basler K.

EMBO J. 2019 Jan 15;38(2). pii: e98873. doi: 10.15252/embj.201798873. Epub 2018 Nov 13.

PMID:
30425074
3.

A reassessment of DNA-immunoprecipitation-based genomic profiling.

Lentini A, Lagerwall C, Vikingsson S, Mjoseng HK, Douvlataniotis K, Vogt H, Green H, Meehan RR, Benson M, Nestor CE.

Nat Methods. 2018 Jul;15(7):499-504. doi: 10.1038/s41592-018-0038-7. Epub 2018 Jun 25.

4.

DNA methylation as a genomic marker of exposure to chemical and environmental agents.

Meehan RR, Thomson JP, Lentini A, Nestor CE, Pennings S.

Curr Opin Chem Biol. 2018 Aug;45:48-56. doi: 10.1016/j.cbpa.2018.02.006. Epub 2018 Mar 2. Review.

5.

LASSIM-A network inference toolbox for genome-wide mechanistic modeling.

Magnusson R, Mariotti GP, Köpsén M, Lövfors W, Gawel DR, Jörnsten R, Linde J, Nordling TEM, Nyman E, Schulze S, Nestor CE, Zhang H, Cedersund G, Benson M, Tjärnberg A, Gustafsson M.

PLoS Comput Biol. 2017 Jun 22;13(6):e1005608. doi: 10.1371/journal.pcbi.1005608. eCollection 2017 Jun.

6.

GAB2 regulates type 2 T helper cell differentiation in humans.

Wang H, Nestor CE, Benson M, Zhang H.

Cytokine. 2017 Aug;96:234-237. doi: 10.1016/j.cyto.2017.04.027. Epub 2017 May 3.

PMID:
28477539
7.

Potential Involvement of Type I Interferon Signaling in Immunotherapy in Seasonal Allergic Rhinitis.

Mattson L, Lentini A, Gawel DR, Badam TV, Benson M, Ledin T, Nestor CE, Gustafsson M, Serra-Musach J, Bjorkander J, Xiang Z, Zhang H.

J Immunol Res. 2016;2016:5153184. doi: 10.1155/2016/5153184. Epub 2016 Dec 19.

8.

Dynamic Response Genes in CD4+ T Cells Reveal a Network of Interactive Proteins that Classifies Disease Activity in Multiple Sclerosis.

Hellberg S, Eklund D, Gawel DR, Köpsén M, Zhang H, Nestor CE, Kockum I, Olsson T, Skogh T, Kastbom A, Sjöwall C, Vrethem M, Håkansson I, Benson M, Jenmalm MC, Gustafsson M, Ernerudh J.

Cell Rep. 2016 Sep 13;16(11):2928-2939. doi: 10.1016/j.celrep.2016.08.036.

9.

5-Hydroxymethylcytosine Remodeling Precedes Lineage Specification during Differentiation of Human CD4(+) T Cells.

Nestor CE, Lentini A, Hägg Nilsson C, Gawel DR, Gustafsson M, Mattson L, Wang H, Rundquist O, Meehan RR, Klocke B, Seifert M, Hauck SM, Laumen H, Zhang H, Benson M.

Cell Rep. 2016 Jul 12;16(2):559-570. doi: 10.1016/j.celrep.2016.05.091. Epub 2016 Jun 23.

10.

A validated gene regulatory network and GWAS identifies early regulators of T cell-associated diseases.

Gustafsson M, Gawel DR, Alfredsson L, Baranzini S, Björkander J, Blomgran R, Hellberg S, Eklund D, Ernerudh J, Kockum I, Konstantinell A, Lahesmaa R, Lentini A, Liljenström HR, Mattson L, Matussek A, Mellergård J, Mendez M, Olsson T, Pujana MA, Rasool O, Serra-Musach J, Stenmarker M, Tripathi S, Viitala M, Wang H, Zhang H, Nestor CE, Benson M.

Sci Transl Med. 2015 Nov 11;7(313):313ra178. doi: 10.1126/scitranslmed.aad2722.

11.

5-Hydroxymethylcytosine Profiling in Human DNA.

Thomson JP, Nestor CE, Meehan RR.

Methods Mol Biol. 2017;1589:89-98. doi: 10.1007/7651_2015_268.

PMID:
26126447
12.

Rapid reprogramming of epigenetic and transcriptional profiles in mammalian culture systems.

Nestor CE, Ottaviano R, Reinhardt D, Cruickshanks HA, Mjoseng HK, McPherson RC, Lentini A, Thomson JP, Dunican DS, Pennings S, Anderton SM, Benson M, Meehan RR.

Genome Biol. 2015 Feb 4;16:11. doi: 10.1186/s13059-014-0576-y.

13.

Modules, networks and systems medicine for understanding disease and aiding diagnosis.

Gustafsson M, Nestor CE, Zhang H, Barabási AL, Baranzini S, Brunak S, Chung KF, Federoff HJ, Gavin AC, Meehan RR, Picotti P, Pujana MÀ, Rajewsky N, Smith KG, Sterk PJ, Villoslada P, Benson M.

Genome Med. 2014 Oct 17;6(10):82. doi: 10.1186/s13073-014-0082-6. eCollection 2014.

14.

Sublingual immunotherapy alters expression of IL-4 and its soluble and membrane-bound receptors.

Nestor CE, Dadfar E, Ernerudh J, Gustafsson M, Björkander J, Benson M, Zhang H.

Allergy. 2014 Nov;69(11):1564-6. doi: 10.1111/all.12505. Epub 2014 Sep 13.

PMID:
25130266
15.

The Allergic Airway Inflammation Repository--a user-friendly, curated resource of mRNA expression levels in studies of allergic airways.

Gawel DR, Rani James A, Benson M, Liljenström R, Muraro A, Nestor CE, Zhang H, Gustafsson M.

Allergy. 2014 Aug;69(8):1115-7. doi: 10.1111/all.12432. Epub 2014 Jun 3.

16.

Integrated genomic and prospective clinical studies show the importance of modular pleiotropy for disease susceptibility, diagnosis and treatment.

Gustafsson M, Edström M, Gawel D, Nestor CE, Wang H, Zhang H, Barrenäs F, Tojo J, Kockum I, Olsson T, Serra-Musach J, Bonifaci N, Pujana MA, Ernerudh J, Benson M.

Genome Med. 2014 Feb 26;6(2):17. doi: 10.1186/gm534. eCollection 2014.

17.

DNA methylation changes separate allergic patients from healthy controls and may reflect altered CD4+ T-cell population structure.

Nestor CE, Barrenäs F, Wang H, Lentini A, Zhang H, Bruhn S, Jörnsten R, Langston MA, Rogers G, Gustafsson M, Benson M.

PLoS Genet. 2014 Jan;10(1):e1004059. doi: 10.1371/journal.pgen.1004059. Epub 2014 Jan 2.

18.

Comparative analysis of affinity-based 5-hydroxymethylation enrichment techniques.

Thomson JP, Hunter JM, Nestor CE, Dunican DS, Terranova R, Moggs JG, Meehan RR.

Nucleic Acids Res. 2013 Dec;41(22):e206. doi: 10.1093/nar/gkt1080. Epub 2013 Nov 7. Erratum in: Nucleic Acids Res. . 2014 Apr;42(6):4142.

19.

Hydroxymethylated DNA immunoprecipitation (hmeDIP).

Nestor CE, Meehan RR.

Methods Mol Biol. 2014;1094:259-67. doi: 10.1007/978-1-62703-706-8_20.

PMID:
24162994
20.

Investigating 5-hydroxymethylcytosine (5hmC): the state of the art.

Nestor CE, Reddington JP, Benson M, Meehan RR.

Methods Mol Biol. 2014;1094:243-58. doi: 10.1007/978-1-62703-706-8_19. Review.

PMID:
24162993
21.

Profiling of human CD4+ T-cell subsets identifies the TH2-specific noncoding RNA GATA3-AS1.

Zhang H, Nestor CE, Zhao S, Lentini A, Bohle B, Benson M, Wang H.

J Allergy Clin Immunol. 2013 Oct;132(4):1005-8. doi: 10.1016/j.jaci.2013.05.033. Epub 2013 Jul 16. No abstract available.

PMID:
23870669
22.

Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes.

Reddington JP, Perricone SM, Nestor CE, Reichmann J, Youngson NA, Suzuki M, Reinhardt D, Dunican DS, Prendergast JG, Mjoseng H, Ramsahoye BH, Whitelaw E, Greally JM, Adams IR, Bickmore WA, Meehan RR.

Genome Biol. 2013 Mar 25;14(3):R25. doi: 10.1186/gb-2013-14-3-r25.

23.

Non-genotoxic carcinogen exposure induces defined changes in the 5-hydroxymethylome.

Thomson JP, Lempiäinen H, Hackett JA, Nestor CE, Müller A, Bolognani F, Oakeley EJ, Schübeler D, Terranova R, Reinhardt D, Moggs JG, Meehan RR.

Genome Biol. 2012 Oct 3;13(10):R93. doi: 10.1186/gb-2012-13-10-r93.

24.

Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns.

Sproul D, Kitchen RR, Nestor CE, Dixon JM, Sims AH, Harrison DJ, Ramsahoye BH, Meehan RR.

Genome Biol. 2012 Oct 3;13(10):R84. doi: 10.1186/gb-2012-13-10-r84.

25.

Promoter DNA methylation couples genome-defence mechanisms to epigenetic reprogramming in the mouse germline.

Hackett JA, Reddington JP, Nestor CE, Dunican DS, Branco MR, Reichmann J, Reik W, Surani MA, Adams IR, Meehan RR.

Development. 2012 Oct;139(19):3623-32. doi: 10.1242/dev.081661.

26.

Correlation of inter-locus polyglutamine toxicity with CAG•CTG triplet repeat expandability and flanking genomic DNA GC content.

Nestor CE, Monckton DG.

PLoS One. 2011;6(12):e28260. doi: 10.1371/journal.pone.0028260. Epub 2011 Dec 6.

27.

Tissue type is a major modifier of the 5-hydroxymethylcytosine content of human genes.

Nestor CE, Ottaviano R, Reddington J, Sproul D, Reinhardt D, Dunican D, Katz E, Dixon JM, Harrison DJ, Meehan RR.

Genome Res. 2012 Mar;22(3):467-77. doi: 10.1101/gr.126417.111. Epub 2011 Nov 21.

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