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Results: 1 to 20 of 24

1.

Identification of TNF-α-Responsive Promoters and Enhancers in the Intestinal Epithelial Cell Model Caco-2.

Boyd M, Coskun M, Lilje B, Andersson R, Hoof I, Bornholdt J, Dahlgaard K, Olsen J, Vitezic M, Bjerrum JT, Seidelin JB, Nielsen OH, Troelsen JT, Sandelin A.

DNA Res. 2014 Jul 2. pii: dsu022. [Epub ahead of print]

PMID:
24990076
[PubMed - as supplied by publisher]
2.

Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation.

Rönnerblad M, Andersson R, Olofsson T, Douagi I, Karimi M, Lehmann S, Hoof I, de Hoon M, Itoh M, Nagao-Sato S, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, Sandelin A, Ekwall K, Arner E, Lennartsson A; FANTOM consortium.

Blood. 2014 Apr 24;123(17):e79-89. doi: 10.1182/blood-2013-02-482893. Epub 2014 Mar 26.

PMID:
24671952
[PubMed - indexed for MEDLINE]
3.

An atlas of active enhancers across human cell types and tissues.

Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F; FANTOM Consortium, Forrest AR, Carninci P, Rehli M, Sandelin A.

Nature. 2014 Mar 27;507(7493):455-61. doi: 10.1038/nature12787.

PMID:
24670763
[PubMed - indexed for MEDLINE]
4.

Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality.

Ntini E, Järvelin AI, Bornholdt J, Chen Y, Boyd M, Jørgensen M, Andersson R, Hoof I, Schein A, Andersen PR, Andersen PK, Preker P, Valen E, Zhao X, Pelechano V, Steinmetz LM, Sandelin A, Jensen TH.

Nat Struct Mol Biol. 2013 Aug;20(8):923-8. doi: 10.1038/nsmb.2640. Epub 2013 Jul 14.

PMID:
23851456
[PubMed - indexed for MEDLINE]
5.

SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments.

Jessen LE, Hoof I, Lund O, Nielsen M.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W286-91. doi: 10.1093/nar/gkt497. Epub 2013 Jun 12.

PMID:
23761454
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Peptide-binding motifs associated with MHC molecules common in Chinese rhesus macaques are analogous to those of human HLA supertypes and include HLA-B27-like alleles.

Mothé BR, Southwood S, Sidney J, English AM, Wriston A, Hoof I, Shabanowitz J, Hunt DF, Sette A.

Immunogenetics. 2013 May;65(5):371-86. doi: 10.1007/s00251-013-0686-9. Epub 2013 Feb 17.

PMID:
23417323
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

CD8+ TCR repertoire formation is guided primarily by the peptide component of the antigenic complex.

Koning D, Costa AI, Hoof I, Miles JJ, Nanlohy NM, Ladell K, Matthews KK, Venturi V, Schellens IM, Borghans JA, Kesmir C, Price DA, van Baarle D.

J Immunol. 2013 Feb 1;190(3):931-9. doi: 10.4049/jimmunol.1202466. Epub 2012 Dec 24.

PMID:
23267020
[PubMed - indexed for MEDLINE]
Free Article
8.

Evolution of HLA-DRB genes.

Doxiadis GG, Hoof I, de Groot N, Bontrop RE.

Mol Biol Evol. 2012 Dec;29(12):3843-53. doi: 10.1093/molbev/mss186. Epub 2012 Jul 23.

PMID:
22826457
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Estimating the fitness cost of escape from HLA presentation in HIV-1 protease and reverse transcriptase.

Mostowy R, Kouyos RD, Hoof I, Hinkley T, Haddad M, Whitcomb JM, Petropoulos CJ, Keşmir C, Bonhoeffer S.

PLoS Comput Biol. 2012;8(5):e1002525. doi: 10.1371/journal.pcbi.1002525. Epub 2012 May 24.

PMID:
22654656
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Proteome sampling by the HLA class I antigen processing pathway.

Hoof I, van Baarle D, Hildebrand WH, Keşmir C.

PLoS Comput Biol. 2012;8(5):e1002517. doi: 10.1371/journal.pcbi.1002517. Epub 2012 May 17.

PMID:
22615552
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

A shared MHC supertype motif emerges by convergent evolution in macaques and mice, but is totally absent in human MHC molecules.

Sette A, Sidney J, Southwood S, Moore C, Berry J, Dow C, Bradley K, Hoof I, Lewis MG, Hildebrand WH, McMurtrey CP, Wilson NA, Watkins DI, Mothé BR.

Immunogenetics. 2012 Jun;64(6):421-34. doi: 10.1007/s00251-011-0598-5. Epub 2012 Feb 10.

PMID:
22322672
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

A comparative analysis of viral peptides presented by contemporary human and chimpanzee MHC class I molecules.

van Deutekom HW, Hoof I, Bontrop RE, Keşmir C.

J Immunol. 2011 Dec 1;187(11):5995-6001. doi: 10.4049/jimmunol.1102236. Epub 2011 Oct 31.

PMID:
22043011
[PubMed - indexed for MEDLINE]
Free Article
13.

HLA class I allele promiscuity revisited.

Rao X, Hoof I, Costa AI, van Baarle D, Keşmir C.

Immunogenetics. 2011 Nov;63(11):691-701. doi: 10.1007/s00251-011-0552-6. Epub 2011 Jun 22.

PMID:
21695550
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Functional analysis of frequently expressed Chinese rhesus macaque MHC class I molecules Mamu-A1*02601 and Mamu-B*08301 reveals HLA-A2 and HLA-A3 supertypic specificities.

Southwood S, Solomon C, Hoof I, Rudersdorf R, Sidney J, Peters B, Wahl A, Hawkins O, Hildebrand W, Mothé BR, Sette A.

Immunogenetics. 2011 May;63(5):275-90. doi: 10.1007/s00251-010-0502-8. Epub 2011 Jan 28.

PMID:
21274527
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

State of the art and challenges in sequence based T-cell epitope prediction.

Lundegaard C, Hoof I, Lund O, Nielsen M.

Immunome Res. 2010 Nov 3;6 Suppl 2:S3. doi: 10.1186/1745-7580-6-S2-S3.

PMID:
21067545
[PubMed]
Free PMC Article
16.

Identification of CD8+ T cell epitopes in the West Nile virus polyprotein by reverse-immunology using NetCTL.

Larsen MV, Lelic A, Parsons R, Nielsen M, Hoof I, Lamberth K, Loeb MB, Buus S, Bramson J, Lund O.

PLoS One. 2010 Sep 14;5(9):e12697. doi: 10.1371/journal.pone.0012697.

PMID:
20856867
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

The most common Chinese rhesus macaque MHC class I molecule shares peptide binding repertoire with the HLA-B7 supertype.

Solomon C, Southwood S, Hoof I, Rudersdorf R, Peters B, Sidney J, Pinilla C, Marcondes MC, Ling B, Marx P, Sette A, Mothé BR.

Immunogenetics. 2010 Jul;62(7):451-64. doi: 10.1007/s00251-010-0450-3. Epub 2010 May 18.

PMID:
20480161
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Interdisciplinary analysis of HIV-specific CD8+ T cell responses against variant epitopes reveals restricted TCR promiscuity.

Hoof I, Pérez CL, Buggert M, Gustafsson RK, Nielsen M, Lund O, Karlsson AC.

J Immunol. 2010 May 1;184(9):5383-91. doi: 10.4049/jimmunol.0903516. Epub 2010 Apr 2.

PMID:
20363973
[PubMed - indexed for MEDLINE]
Free Article
19.

The MHC motif viewer: a visualization tool for MHC binding motifs.

Rapin N, Hoof I, Lund O, Nielsen M.

Curr Protoc Immunol. 2010 Feb;Chapter 18:Unit 18.17. doi: 10.1002/0471142735.im1817s88.

PMID:
20143317
[PubMed - indexed for MEDLINE]
20.

The immune epitope database 2.0.

Vita R, Zarebski L, Greenbaum JA, Emami H, Hoof I, Salimi N, Damle R, Sette A, Peters B.

Nucleic Acids Res. 2010 Jan;38(Database issue):D854-62. doi: 10.1093/nar/gkp1004. Epub 2009 Nov 11.

PMID:
19906713
[PubMed - indexed for MEDLINE]
Free PMC Article

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