Ukkonen E - Search Results

1

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

2

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

3

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.

4

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

5

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.

6

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

7

Fast motif matching revisited: high-order PWMs, SNPs and indels.

Korhonen JH, Palin K, Taipale J, Ukkonen E. Korhonen JH, et al. Among authors: ukkonen e. Bioinformatics. 2017 Feb 15;33(4):514-521. doi: 10.1093/bioinformatics/btw683. Bioinformatics. 2017. PMID: 28011774

8

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.

9

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.

10

Discovering patterns and subfamilies in biosequences.

Brazma A, Jonassen I, Ukkonen E, Vilo J. Brazma A, et al. Among authors: ukkonen e. Proc Int Conf Intell Syst Mol Biol. 1996;4:34-43. Proc Int Conf Intell Syst Mol Biol. 1996. PMID: 8877502 Review.

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