Ukkonen E - Search Results

1

Integrating sequence, evolution and functional genomics in regulatory genomics.

Vingron M, Brazma A, Coulson R, van Helden J, Manke T, Palin K, Sand O, Ukkonen E. Vingron M, et al. Among authors: ukkonen e. Genome Biol. 2009;10(1):202. doi: 10.1186/gb-2009-10-1-202. Epub 2009 Jan 30. Genome Biol. 2009. PMID: 19226437 Free PMC article. Review.

2

Predicting gene regulatory elements in silico on a genomic scale.

Brazma A, Jonassen I, Vilo J, Ukkonen E. Brazma A, et al. Among authors: ukkonen e. Genome Res. 1998 Nov;8(11):1202-15. doi: 10.1101/gr.8.11.1202. Genome Res. 1998. PMID: 9847082 Free PMC article.

3

From gene networks to gene function.

Schlitt T, Palin K, Rung J, Dietmann S, Lappe M, Ukkonen E, Brazma A. Schlitt T, et al. Among authors: ukkonen e. Genome Res. 2003 Dec;13(12):2568-76. doi: 10.1101/gr.1111403. Genome Res. 2003. PMID: 14656964 Free PMC article.

4

Locating potential enhancer elements by comparative genomics using the EEL software.

Palin K, Taipale J, Ukkonen E. Palin K, et al. Among authors: ukkonen e. Nat Protoc. 2006;1(1):368-74. doi: 10.1038/nprot.2006.56. Nat Protoc. 2006. PMID: 17406258

5

The BREW workshop series: a stimulating experience in PhD education.

Giegerich R, Brazma A, Jonassen I, Ukkonen E, Vingron M. Giegerich R, et al. Among authors: ukkonen e. Brief Bioinform. 2008 May;9(3):250-3. doi: 10.1093/bib/bbn002. Epub 2008 Jan 23. Brief Bioinform. 2008. PMID: 18216087

6

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities.

Jolma A, Kivioja T, Toivonen J, Cheng L, Wei G, Enge M, Taipale M, Vaquerizas JM, Yan J, Sillanpää MJ, Bonke M, Palin K, Talukder S, Hughes TR, Luscombe NM, Ukkonen E, Taipale J. Jolma A, et al. Among authors: ukkonen e. Genome Res. 2010 Jun;20(6):861-73. doi: 10.1101/gr.100552.109. Epub 2010 Apr 8. Genome Res. 2010. PMID: 20378718 Free PMC article.

7

Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity.

Hallikas O, Palin K, Sinjushina N, Rautiainen R, Partanen J, Ukkonen E, Taipale J. Hallikas O, et al. Among authors: ukkonen e. Cell. 2006 Jan 13;124(1):47-59. doi: 10.1016/j.cell.2005.10.042. Cell. 2006. PMID: 16413481 Free article.

8

Correlating gene promoters and expression in gene disruption experiments.

Palin K, Ukkonen E, Brazma A, Vilo J. Palin K, et al. Among authors: ukkonen e. Bioinformatics. 2002;18 Suppl 2:S172-80. doi: 10.1093/bioinformatics/18.suppl_2.s172. Bioinformatics. 2002. PMID: 12386000

9

Data mining for regulatory elements in yeast genome.

Brazma A, Vilo J, Ukkonen E, Valtonen K. Brazma A, et al. Among authors: ukkonen e. Proc Int Conf Intell Syst Mol Biol. 1997;5:65-74. Proc Int Conf Intell Syst Mol Biol. 1997. PMID: 9322017

10

Mining for putative regulatory elements in the yeast genome using gene expression data.

Vilo J, Brazma A, Jonassen I, Robinson A, Ukkonen E. Vilo J, et al. Among authors: ukkonen e. Proc Int Conf Intell Syst Mol Biol. 2000;8:384-94. Proc Int Conf Intell Syst Mol Biol. 2000. PMID: 10977099

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