Ukkonen E - Search Results

1

DNA-binding specificities of human transcription factors.

Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei G, Palin K, Vaquerizas JM, Vincentelli R, Luscombe NM, Hughes TR, Lemaire P, Ukkonen E, Kivioja T, Taipale J. Jolma A, et al. Among authors: ukkonen e. Cell. 2013 Jan 17;152(1-2):327-39. doi: 10.1016/j.cell.2012.12.009. Cell. 2013. PMID: 23332764 Free article.

2

Modular discovery of monomeric and dimeric transcription factor binding motifs for large data sets.

Toivonen J, Kivioja T, Jolma A, Yin Y, Taipale J, Ukkonen E. Toivonen J, et al. Among authors: ukkonen e. Nucleic Acids Res. 2018 May 4;46(8):e44. doi: 10.1093/nar/gky027. Nucleic Acids Res. 2018. PMID: 29385521 Free PMC article.

3

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.

4

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.

5

MODER2: first-order Markov modeling and discovery of monomeric and dimeric binding motifs.

Toivonen J, Das PK, Taipale J, Ukkonen E. Toivonen J, et al. Among authors: ukkonen e. Bioinformatics. 2020 May 1;36(9):2690-2696. doi: 10.1093/bioinformatics/btaa045. Bioinformatics. 2020. PMID: 31999322 Free PMC article.

6

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo.

Wei GH, Badis G, Berger MF, Kivioja T, Palin K, Enge M, Bonke M, Jolma A, Varjosalo M, Gehrke AR, Yan J, Talukder S, Turunen M, Taipale M, Stunnenberg HG, Ukkonen E, Hughes TR, Bulyk ML, Taipale J. Wei GH, et al. Among authors: ukkonen e. EMBO J. 2010 Jul 7;29(13):2147-60. doi: 10.1038/emboj.2010.106. Epub 2010 Jun 1. EMBO J. 2010. PMID: 20517297 Free PMC article.

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

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

9

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

10

Finding significant matches of position weight matrices in linear time.

Pizzi C, Rastas P, Ukkonen E. Pizzi C, et al. Among authors: ukkonen e. IEEE/ACM Trans Comput Biol Bioinform. 2011 Jan-Mar;8(1):69-79. doi: 10.1109/TCBB.2009.35. IEEE/ACM Trans Comput Biol Bioinform. 2011. PMID: 21071798

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