Holm L - Search Results

1

Li J, Besseau S, Törönen P, Sipari N, Kollist H, Holm L, Palva ET. Li J, et al. Among authors: holm l. New Phytol. 2013 Oct;200(2):457-472. doi: 10.1111/nph.12378. Epub 2013 Jul 1. New Phytol. 2013. PMID: 23815736 Free PMC article.

2

POXO: a web-enabled tool series to discover transcription factor binding sites.

Kankainen M, Pehkonen P, Rosenstöm P, Törönen P, Wong G, Holm L. Kankainen M, et al. Among authors: holm l. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W534-40. doi: 10.1093/nar/gkl296. Nucleic Acids Res. 2006. PMID: 16845065 Free PMC article.

3

Bayesian search of functionally divergent protein subgroups and their function specific residues.

Marttinen P, Corander J, Törönen P, Holm L. Marttinen P, et al. Among authors: holm l. Bioinformatics. 2006 Oct 15;22(20):2466-74. doi: 10.1093/bioinformatics/btl411. Epub 2006 Jul 26. Bioinformatics. 2006. PMID: 16870932

4

Identifying functional gene sets from hierarchically clustered expression data: map of abiotic stress regulated genes in Arabidopsis thaliana.

Kankainen M, Brader G, Törönen P, Palva ET, Holm L. Kankainen M, et al. Among authors: holm l. Nucleic Acids Res. 2006;34(18):e124. doi: 10.1093/nar/gkl694. Epub 2006 Sep 26. Nucleic Acids Res. 2006. PMID: 17003050 Free PMC article.

5

Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function.

Törönen P, Ojala PJ, Marttinen P, Holm L. Törönen P, et al. Among authors: holm l. BMC Bioinformatics. 2009 Sep 23;10:307. doi: 10.1186/1471-2105-10-307. BMC Bioinformatics. 2009. PMID: 19775443 Free PMC article.

6

Generation of Gene Ontology benchmark datasets with various types of positive signal.

Törönen P, Pehkonen P, Holm L. Törönen P, et al. Among authors: holm l. BMC Bioinformatics. 2009 Oct 7;10:319. doi: 10.1186/1471-2105-10-319. BMC Bioinformatics. 2009. PMID: 19811632 Free PMC article.

7

Revised phylogeny and novel horizontally acquired virulence determinants of the model soft rot phytopathogen Pectobacterium wasabiae SCC3193.

Nykyri J, Niemi O, Koskinen P, Nokso-Koivisto J, Pasanen M, Broberg M, Plyusnin I, Törönen P, Holm L, Pirhonen M, Palva ET. Nykyri J, et al. Among authors: holm l. PLoS Pathog. 2012;8(11):e1003013. doi: 10.1371/journal.ppat.1003013. Epub 2012 Nov 1. PLoS Pathog. 2012. PMID: 23133391 Free PMC article.

8

GOParGenPy: a high throughput method to generate gene ontology data matrices.

Kumar AA, Holm L, Toronen P. Kumar AA, et al. Among authors: holm l. BMC Bioinformatics. 2013 Aug 8;14:242. doi: 10.1186/1471-2105-14-242. BMC Bioinformatics. 2013. PMID: 23927037 Free PMC article.

9

Gene set analysis: limitations in popular existing methods and proposed improvements.

Mishra P, Törönen P, Leino Y, Holm L. Mishra P, et al. Among authors: holm l. Bioinformatics. 2014 Oct;30(19):2747-56. doi: 10.1093/bioinformatics/btu374. Epub 2014 Jun 5. Bioinformatics. 2014. PMID: 24903419

10

PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment.

Koskinen P, Törönen P, Nokso-Koivisto J, Holm L. Koskinen P, et al. Among authors: holm l. Bioinformatics. 2015 May 15;31(10):1544-52. doi: 10.1093/bioinformatics/btu851. Epub 2015 Jan 8. Bioinformatics. 2015. PMID: 25653249

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