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Items: 1 to 20 of 94

1.

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

Baillie JK, Bretherick A, Haley CS, Clohisey S, Gray A, Neyton LPA, Barrett J, Stahl EA, Tenesa A, Andersson R, Brown JB, Faulkner GJ, Lizio M, Schaefer U, Daub C, Itoh M, Kondo N, Lassmann T, Kawai J; IIBDGC Consortium, Mole D, Bajic VB, Heutink P, Rehli M, Kawaji H, Sandelin A, Suzuki H, Satsangi J, Wells CA, Hacohen N, Freeman TC, Hayashizaki Y, Carninci P, Forrest ARR, Hume DA.

PLoS Comput Biol. 2018 Mar 1;14(3):e1005934. doi: 10.1371/journal.pcbi.1005934. eCollection 2018 Mar.

2.

An integrative functional genomics framework for effective identification of novel regulatory variants in genome-phenome studies.

Zhao J, Cheng F, Jia P, Cox N, Denny JC, Zhao Z.

Genome Med. 2018 Jan 29;10(1):7. doi: 10.1186/s13073-018-0513-x.

3.

Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits.

Corradin O, Saiakhova A, Akhtar-Zaidi B, Myeroff L, Willis J, Cowper-Sal lari R, Lupien M, Markowitz S, Scacheri PC.

Genome Res. 2014 Jan;24(1):1-13. doi: 10.1101/gr.164079.113. Epub 2013 Nov 6.

4.

An atlas of human long non-coding RNAs with accurate 5' ends.

Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, Denisenko E, Schmeier S, Poulsen TM, Severin J, Lizio M, Kawaji H, Kasukawa T, Itoh M, Burroughs AM, Noma S, Djebali S, Alam T, Medvedeva YA, Testa AC, Lipovich L, Yip CW, Abugessaisa I, Mendez M, Hasegawa A, Tang D, Lassmann T, Heutink P, Babina M, Wells CA, Kojima S, Nakamura Y, Suzuki H, Daub CO, de Hoon MJ, Arner E, Hayashizaki Y, Carninci P, Forrest AR.

Nature. 2017 Mar 9;543(7644):199-204. doi: 10.1038/nature21374. Epub 2017 Mar 1.

PMID:
28241135
5.

Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease.

Baillie JK, Arner E, Daub C, De Hoon M, Itoh M, Kawaji H, Lassmann T, Carninci P, Forrest AR, Hayashizaki Y; FANTOM Consortium, Faulkner GJ, Wells CA, Rehli M, Pavli P, Summers KM, Hume DA.

PLoS Genet. 2017 Mar 6;13(3):e1006641. doi: 10.1371/journal.pgen.1006641. eCollection 2017 Mar.

6.
7.

Topological analysis of metabolic networks integrating co-segregating transcriptomes and metabolomes in type 2 diabetic rat congenic series.

Dumas ME, Domange C, Calderari S, Martínez AR, Ayala R, Wilder SP, Suárez-Zamorano N, Collins SC, Wallis RH, Gu Q, Wang Y, Hue C, Otto GW, Argoud K, Navratil V, Mitchell SC, Lindon JC, Holmes E, Cazier JB, Nicholson JK, Gauguier D.

Genome Med. 2016 Sep 30;8(1):101.

8.

Sequential regulatory activity prediction across chromosomes with convolutional neural networks.

Kelley DR, Reshef YA, Bileschi M, Belanger D, McLean CY, Snoek J.

Genome Res. 2018 May;28(5):739-750. doi: 10.1101/gr.227819.117. Epub 2018 Mar 27.

9.

Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations.

Nica AC, Montgomery SB, Dimas AS, Stranger BE, Beazley C, Barroso I, Dermitzakis ET.

PLoS Genet. 2010 Apr 1;6(4):e1000895. doi: 10.1371/journal.pgen.1000895.

10.

Putative enhancer sites in the bovine genome are enriched with variants affecting complex traits.

Wang M, Hancock TP, MacLeod IM, Pryce JE, Cocks BG, Hayes BJ.

Genet Sel Evol. 2017 Jul 6;49(1):56. doi: 10.1186/s12711-017-0331-4.

11.

Integrative analysis of omics summary data reveals putative mechanisms underlying complex traits.

Wu Y, Zeng J, Zhang F, Zhu Z, Qi T, Zheng Z, Lloyd-Jones LR, Marioni RE, Martin NG, Montgomery GW, Deary IJ, Wray NR, Visscher PM, McRae AF, Yang J.

Nat Commun. 2018 Mar 2;9(1):918. doi: 10.1038/s41467-018-03371-0.

12.

Predicting distinct organization of transcription factor binding sites on the promoter regions: a new genome-based approach to expand human embryonic stem cell regulatory network.

Hosseinpour B, Bakhtiarizadeh MR, Khosravi P, Ebrahimie E.

Gene. 2013 Dec 1;531(2):212-9. doi: 10.1016/j.gene.2013.09.011. Epub 2013 Sep 13.

PMID:
24042128
13.

Integrated genomics of susceptibility to alkylator-induced leukemia in mice.

Cahan P, Graubert TA.

BMC Genomics. 2010 Nov 17;11:638. doi: 10.1186/1471-2164-11-638.

14.

Large-scale East-Asian eQTL mapping reveals novel candidate genes for LD mapping and the genomic landscape of transcriptional effects of sequence variants.

Narahara M, Higasa K, Nakamura S, Tabara Y, Kawaguchi T, Ishii M, Matsubara K, Matsuda F, Yamada R.

PLoS One. 2014 Jun 23;9(6):e100924. doi: 10.1371/journal.pone.0100924. eCollection 2014.

15.

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters.

Javierre BM, Burren OS, Wilder SP, Kreuzhuber R, Hill SM, Sewitz S, Cairns J, Wingett SW, Várnai C, Thiecke MJ, Burden F, Farrow S, Cutler AJ, Rehnström K, Downes K, Grassi L, Kostadima M, Freire-Pritchett P, Wang F; BLUEPRINT Consortium, Stunnenberg HG, Todd JA, Zerbino DR, Stegle O, Ouwehand WH, Frontini M, Wallace C, Spivakov M, Fraser P.

Cell. 2016 Nov 17;167(5):1369-1384.e19. doi: 10.1016/j.cell.2016.09.037.

16.

Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets.

Xiong Q, Ancona N, Hauser ER, Mukherjee S, Furey TS.

Genome Res. 2012 Feb;22(2):386-97. doi: 10.1101/gr.124370.111. Epub 2011 Sep 22. Erratum in: Genome Res. 2013 May;23(5):905.

17.

Genetic studies of Crohn's disease: past, present and future.

Liu JZ, Anderson CA.

Best Pract Res Clin Gastroenterol. 2014 Jun;28(3):373-86. doi: 10.1016/j.bpg.2014.04.009. Epub 2014 May 6. Review.

18.

Mapping the genetic architecture of gene expression in human liver.

Schadt EE, Molony C, Chudin E, Hao K, Yang X, Lum PY, Kasarskis A, Zhang B, Wang S, Suver C, Zhu J, Millstein J, Sieberts S, Lamb J, GuhaThakurta D, Derry J, Storey JD, Avila-Campillo I, Kruger MJ, Johnson JM, Rohl CA, van Nas A, Mehrabian M, Drake TA, Lusis AJ, Smith RC, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, Ulrich R.

PLoS Biol. 2008 May 6;6(5):e107. doi: 10.1371/journal.pbio.0060107.

19.

A comprehensive analysis of shared loci between systemic lupus erythematosus (SLE) and sixteen autoimmune diseases reveals limited genetic overlap.

Ramos PS, Criswell LA, Moser KL, Comeau ME, Williams AH, Pajewski NM, Chung SA, Graham RR, Zidovetzki R, Kelly JA, Kaufman KM, Jacob CO, Vyse TJ, Tsao BP, Kimberly RP, Gaffney PM, Alarcón-Riquelme ME, Harley JB, Langefeld CD; International Consortium on the Genetics of Systemic Erythematosus.

PLoS Genet. 2011 Dec;7(12):e1002406. doi: 10.1371/journal.pgen.1002406. Epub 2011 Dec 8.

20.

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