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Items: 12

1.

RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.

Uyar B, Yusuf D, Wurmus R, Rajewsky N, Ohler U, Akalin A.

Nucleic Acids Res. 2017 Jun 2;45(10):e91. doi: 10.1093/nar/gkx120.

2.

Degrons in cancer.

Mészáros B, Kumar M, Gibson TJ, Uyar B, Dosztányi Z.

Sci Signal. 2017 Mar 14;10(470). pii: eaak9982. doi: 10.1126/scisignal.aak9982. Review.

PMID:
28292960
3.

ELM 2016--data update and new functionality of the eukaryotic linear motif resource.

Dinkel H, Van Roey K, Michael S, Kumar M, Uyar B, Altenberg B, Milchevskaya V, Schneider M, Kühn H, Behrendt A, Dahl SL, Damerell V, Diebel S, Kalman S, Klein S, Knudsen AC, Mäder C, Merrill S, Staudt A, Thiel V, Welti L, Davey NE, Diella F, Gibson TJ.

Nucleic Acids Res. 2016 Jan 4;44(D1):D294-300. doi: 10.1093/nar/gkv1291. Epub 2015 Nov 28.

4.

How pathogens use linear motifs to perturb host cell networks.

Via A, Uyar B, Brun C, Zanzoni A.

Trends Biochem Sci. 2015 Jan;40(1):36-48. doi: 10.1016/j.tibs.2014.11.001. Epub 2014 Dec 1. Review.

PMID:
25475989
5.

Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer?

Uyar B, Weatheritt RJ, Dinkel H, Davey NE, Gibson TJ.

Mol Biosyst. 2014 Oct;10(10):2626-42. doi: 10.1039/c4mb00290c.

6.

Short linear motifs: ubiquitous and functionally diverse protein interaction modules directing cell regulation.

Van Roey K, Uyar B, Weatheritt RJ, Dinkel H, Seiler M, Budd A, Gibson TJ, Davey NE.

Chem Rev. 2014 Jul 9;114(13):6733-78. doi: 10.1021/cr400585q. Epub 2014 Jun 13. Review. No abstract available.

PMID:
24926813
7.

The eukaryotic linear motif resource ELM: 10 years and counting.

Dinkel H, Van Roey K, Michael S, Davey NE, Weatheritt RJ, Born D, Speck T, Krüger D, Grebnev G, Kuban M, Strumillo M, Uyar B, Budd A, Altenberg B, Seiler M, Chemes LB, Glavina J, Sánchez IE, Diella F, Gibson TJ.

Nucleic Acids Res. 2014 Jan;42(Database issue):D259-66. doi: 10.1093/nar/gkt1047. Epub 2013 Nov 7.

8.

RNA-seq analysis of the C. briggsae transcriptome.

Uyar B, Chu JS, Vergara IA, Chua SY, Jones MR, Wong T, Baillie DL, Chen N.

Genome Res. 2012 Aug;22(8):1567-80. doi: 10.1101/gr.134601.111. Epub 2012 Jul 6.

9.

ELM--the database of eukaryotic linear motifs.

Dinkel H, Michael S, Weatheritt RJ, Davey NE, Van Roey K, Altenberg B, Toedt G, Uyar B, Seiler M, Budd A, Jödicke L, Dammert MA, Schroeter C, Hammer M, Schmidt T, Jehl P, McGuigan C, Dymecka M, Chica C, Luck K, Via A, Chatr-Aryamontri A, Haslam N, Grebnev G, Edwards RJ, Steinmetz MO, Meiselbach H, Diella F, Gibson TJ.

Nucleic Acids Res. 2012 Jan;40(Database issue):D242-51. doi: 10.1093/nar/gkr1064. Epub 2011 Nov 21.

10.

Attributes of short linear motifs.

Davey NE, Van Roey K, Weatheritt RJ, Toedt G, Uyar B, Altenberg B, Budd A, Diella F, Dinkel H, Gibson TJ.

Mol Biosyst. 2012 Jan;8(1):268-81. doi: 10.1039/c1mb05231d. Epub 2011 Sep 12.

PMID:
21909575
11.

Fine tuning of RFX/DAF-19-regulated target gene expression through binding to multiple sites in Caenorhabditis elegans.

Chu JS, Tarailo-Graovac M, Zhang D, Wang J, Uyar B, Tu D, Trinh J, Baillie DL, Chen N.

Nucleic Acids Res. 2012 Jan;40(1):53-64. doi: 10.1093/nar/gkr690. Epub 2011 Sep 8.

12.

genBlastG: using BLAST searches to build homologous gene models.

She R, Chu JS, Uyar B, Wang J, Wang K, Chen N.

Bioinformatics. 2011 Aug 1;27(15):2141-3. doi: 10.1093/bioinformatics/btr342. Epub 2011 Jun 8.

PMID:
21653517

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