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Items: 1 to 20 of 98

1.

Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies.

Boyd M, Thodberg M, Vitezic M, Bornholdt J, Vitting-Seerup K, Chen Y, Coskun M, Li Y, Lo BZS, Klausen P, Jan Schweiger P, Pedersen AG, Rapin N, Skovgaard K, Dahlgaard K, Andersson R, Terkelsen TB, Lilje B, Troelsen JT, Petersen AM, Jensen KB, Gögenur I, Thielsen P, Seidelin JB, Nielsen OH, Bjerrum JT, Sandelin A.

Nat Commun. 2018 Apr 25;9(1):1661. doi: 10.1038/s41467-018-03766-z.

2.

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.

3.

Relation between NOD2 genotype and changes in innate signaling in Crohn's disease on mRNA and miRNA levels.

Chen Y, Salem M, Boyd M, Bornholdt J, Li Y, Coskun M, Seidelin JB, Sandelin A, Nielsen OH.

NPJ Genom Med. 2017 Feb 8;2:3. doi: 10.1038/s41525-016-0001-4. eCollection 2017.

4.

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.

Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, Bessy A, Chèneby J, Kulkarni SR, Tan G, Baranasic D, Arenillas DJ, Sandelin A, Vandepoele K, Lenhard B, Ballester B, Wasserman WW, Parcy F, Mathelier A.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1284. doi: 10.1093/nar/gkx1188. No abstract available.

5.

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.

Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, Bessy A, Chèneby J, Kulkarni SR, Tan G, Baranasic D, Arenillas DJ, Sandelin A, Vandepoele K, Lenhard B, Ballester B, Wasserman WW, Parcy F, Mathelier A.

Nucleic Acids Res. 2018 Jan 4;46(D1):D260-D266. doi: 10.1093/nar/gkx1126.

6.

An integrated expression atlas of miRNAs and their promoters in human and mouse.

de Rie D, Abugessaisa I, Alam T, Arner E, Arner P, Ashoor H, Åström G, Babina M, Bertin N, Burroughs AM, Carlisle AJ, Daub CO, Detmar M, Deviatiiarov R, Fort A, Gebhard C, Goldowitz D, Guhl S, Ha TJ, Harshbarger J, Hasegawa A, Hashimoto K, Herlyn M, Heutink P, Hitchens KJ, Hon CC, Huang E, Ishizu Y, Kai C, Kasukawa T, Klinken P, Lassmann T, Lecellier CH, Lee W, Lizio M, Makeev V, Mathelier A, Medvedeva YA, Mejhert N, Mungall CJ, Noma S, Ohshima M, Okada-Hatakeyama M, Persson H, Rizzu P, Roudnicky F, Sætrom P, Sato H, Severin J, Shin JW, Swoboda RK, Tarui H, Toyoda H, Vitting-Seerup K, Winteringham L, Yamaguchi Y, Yasuzawa K, Yoneda M, Yumoto N, Zabierowski S, Zhang PG, Wells CA, Summers KM, Kawaji H, Sandelin A, Rehli M; FANTOM Consortium, Hayashizaki Y, Carninci P, Forrest ARR, de Hoon MJL.

Nat Biotechnol. 2017 Sep;35(9):872-878. doi: 10.1038/nbt.3947. Epub 2017 Aug 21.

7.

Oxygen-induced impairment in arterial function is corrected by slow breathing in patients with type 1 diabetes.

Bernardi L, Gordin D, Bordino M, Rosengård-Bärlund M, Sandelin A, Forsblom C, Groop PH.

Sci Rep. 2017 Jul 20;7(1):6001. doi: 10.1038/s41598-017-04947-4.

8.

The Landscape of Isoform Switches in Human Cancers.

Vitting-Seerup K, Sandelin A.

Mol Cancer Res. 2017 Sep;15(9):1206-1220. doi: 10.1158/1541-7786.MCR-16-0459. Epub 2017 Jun 5.

PMID:
28584021
9.

Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo.

Bornholdt J, Saber AT, Lilje B, Boyd M, Jørgensen M, Chen Y, Vitezic M, Jacobsen NR, Poulsen SS, Berthing T, Bressendorff S, Vitting-Seerup K, Andersson R, Hougaard KS, Yauk CL, Halappanavar S, Wallin H, Vogel U, Sandelin A.

ACS Nano. 2017 Apr 25;11(4):3597-3613. doi: 10.1021/acsnano.6b07533. Epub 2017 Mar 31.

PMID:
28345861
10.

On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase.

Ienasescu H, Li K, Andersson R, Vitezic M, Rennie S, Chen Y, Vitting-Seerup K, Lagoni E, Boyd M, Bornholdt J, de Hoon MJ, Kawaji H, Lassmann T; FANTOM Consortium, Hayashizaki Y, Forrest AR, Carninci P, Sandelin A.

Database (Oxford). 2016 Dec 26;2016. pii: baw144. doi: 10.1093/database/baw144. Print 2016.

11.

Identification of a Nuclear Exosome Decay Pathway for Processed Transcripts.

Meola N, Domanski M, Karadoulama E, Chen Y, Gentil C, Pultz D, Vitting-Seerup K, Lykke-Andersen S, Andersen JS, Sandelin A, Jensen TH.

Mol Cell. 2016 Nov 3;64(3):520-533. doi: 10.1016/j.molcel.2016.09.025. Epub 2016 Oct 27.

12.

Transcriptional Dynamics During Human Adipogenesis and Its Link to Adipose Morphology and Distribution.

Ehrlund A, Mejhert N, Björk C, Andersson R, Kulyté A, Åström G, Itoh M, Kawaji H, Lassmann T, Daub CO, Carninci P, Forrest AR, Hayashizaki Y, Sandelin A, Ingelsson E; FANTOM Consortium, Rydén M, Laurencikiene J, Arner P, Arner E.

Diabetes. 2017 Jan;66(1):218-230. doi: 10.2337/db16-0631. Epub 2016 Nov 1.

13.

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals.

Lizio M, Harshbarger J, Abugessaisa I, Noguchi S, Kondo A, Severin J, Mungall C, Arenillas D, Mathelier A, Medvedeva YA, Lennartsson A, Drabløs F, Ramilowski JA, Rackham O, Gough J, Andersson R, Sandelin A, Ienasescu H, Ono H, Bono H, Hayashizaki Y, Carninci P, Forrest AR, Kasukawa T, Kawaji H.

Nucleic Acids Res. 2017 Jan 4;45(D1):D737-D743. doi: 10.1093/nar/gkw995. Epub 2016 Oct 27.

14.

The Adipose Transcriptional Response to Insulin Is Determined by Obesity, Not Insulin Sensitivity.

Rydén M, Hrydziuszko O, Mileti E, Raman A, Bornholdt J, Boyd M, Toft E, Qvist V, Näslund E, Thorell A, Andersson DP, Dahlman I, Gao H, Sandelin A, Daub CO, Arner P.

Cell Rep. 2016 Aug 30;16(9):2317-26. doi: 10.1016/j.celrep.2016.07.070. Epub 2016 Aug 18.

15.

Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters.

Chen Y, Pai AA, Herudek J, Lubas M, Meola N, Järvelin AI, Andersson R, Pelechano V, Steinmetz LM, Jensen TH, Sandelin A.

Nat Genet. 2016 Sep;48(9):984-94. doi: 10.1038/ng.3616. Epub 2016 Jul 25.

16.

Regulation of Laminin γ2 Expression by CDX2 in Colonic Epithelial Cells Is Impaired During Active Inflammation.

Coskun M, Soendergaard C, Joergensen S, Dahlgaard K, Riis LB, Nielsen OH, Sandelin A, Troelsen JT.

J Cell Biochem. 2017 Feb;118(2):298-307. doi: 10.1002/jcb.25636. Epub 2016 Jun 29.

PMID:
27333824
17.

Corrigendum: Human nonsense-mediated RNA decay initiates widely by endonucleolysis and targets snoRNA host genes.

Lykke-Andersen S, Chen Y, Ardal BR, Lilje B, Waage J, Sandelin A, Jensen TH.

Genes Dev. 2016 May 1;30(9):1128-34. doi: 10.1101/gad.281881.116. No abstract available.

18.

Regulating retrotransposon activity through the use of alternative transcription start sites.

Persson J, Steglich B, Smialowska A, Boyd M, Bornholdt J, Andersson R, Schurra C, Arcangioli B, Sandelin A, Nielsen O, Ekwall K.

EMBO Rep. 2016 May;17(5):753-68. doi: 10.15252/embr.201541866. Epub 2016 Feb 22.

19.

Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors.

Lennartsson A, Arner E, Fagiolini M, Saxena A, Andersson R, Takahashi H, Noro Y, Sng J, Sandelin A, Hensch TK, Carninci P.

Epigenetics Chromatin. 2015 Dec 14;8:55. doi: 10.1186/s13072-015-0043-3. eCollection 2015.

20.

Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers.

Kaczkowski B, Tanaka Y, Kawaji H, Sandelin A, Andersson R, Itoh M, Lassmann T, Hayashizaki Y, Carninci P, Forrest AR; FANTOM5 Consortium.

Cancer Res. 2016 Jan 15;76(2):216-26. doi: 10.1158/0008-5472.CAN-15-0484. Epub 2015 Nov 9.

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