Honkela A - Search Results

1

Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.

wa Maina C, Honkela A, Matarese F, Grote K, Stunnenberg HG, Reid G, Lawrence ND, Rattray M. wa Maina C, et al. Among authors: honkela a. PLoS Comput Biol. 2014 May 15;10(5):e1003598. doi: 10.1371/journal.pcbi.1003598. eCollection 2014 May. PLoS Comput Biol. 2014. PMID: 24830797 Free PMC article.

2

Mining regulatory network connections by ranking transcription factor target genes using time series expression data.

Honkela A, Rattray M, Lawrence ND. Honkela A, et al. Methods Mol Biol. 2013;939:59-67. doi: 10.1007/978-1-62703-107-3_6. Methods Mol Biol. 2013. PMID: 23192541

3

Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays.

Honkela A, Peltonen J, Topa H, Charapitsa I, Matarese F, Grote K, Stunnenberg HG, Reid G, Lawrence ND, Rattray M. Honkela A, et al. Proc Natl Acad Sci U S A. 2015 Oct 20;112(42):13115-20. doi: 10.1073/pnas.1420404112. Epub 2015 Oct 5. Proc Natl Acad Sci U S A. 2015. PMID: 26438844 Free PMC article.

4

Gaussian process modelling of latent chemical species: applications to inferring transcription factor activities.

Gao P, Honkela A, Rattray M, Lawrence ND. Gao P, et al. Among authors: honkela a. Bioinformatics. 2008 Aug 15;24(16):i70-5. doi: 10.1093/bioinformatics/btn278. Bioinformatics. 2008. PMID: 18689843

5

Model-based method for transcription factor target identification with limited data.

Honkela A, Girardot C, Gustafson EH, Liu YH, Furlong EE, Lawrence ND, Rattray M. Honkela A, et al. Proc Natl Acad Sci U S A. 2010 Apr 27;107(17):7793-8. doi: 10.1073/pnas.0914285107. Epub 2010 Apr 12. Proc Natl Acad Sci U S A. 2010. PMID: 20385836 Free PMC article.

6

tigre: Transcription factor inference through gaussian process reconstruction of expression for bioconductor.

Honkela A, Gao P, Ropponen J, Rattray M, Lawrence ND. Honkela A, et al. Bioinformatics. 2011 Apr 1;27(7):1026-7. doi: 10.1093/bioinformatics/btr057. Epub 2011 Feb 7. Bioinformatics. 2011. PMID: 21300702

7

Identifying differentially expressed transcripts from RNA-seq data with biological variation.

Glaus P, Honkela A, Rattray M. Glaus P, et al. Among authors: honkela a. Bioinformatics. 2012 Jul 1;28(13):1721-8. doi: 10.1093/bioinformatics/bts260. Epub 2012 May 3. Bioinformatics. 2012. PMID: 22563066 Free PMC article.

8

Fast and accurate approximate inference of transcript expression from RNA-seq data.

Hensman J, Papastamoulis P, Glaus P, Honkela A, Rattray M. Hensman J, et al. Among authors: honkela a. Bioinformatics. 2015 Dec 15;31(24):3881-9. doi: 10.1093/bioinformatics/btv483. Epub 2015 Aug 26. Bioinformatics. 2015. PMID: 26315907 Free PMC article.

9

Predicting stimulation-dependent enhancer-promoter interactions from ChIP-Seq time course data.

Dzida T, Iqbal M, Charapitsa I, Reid G, Stunnenberg H, Matarese F, Grote K, Honkela A, Rattray M. Dzida T, et al. Among authors: honkela a. PeerJ. 2017 Sep 28;5:e3742. doi: 10.7717/peerj.3742. eCollection 2017. PeerJ. 2017. PMID: 28970965 Free PMC article.

10

Identifying targets of multiple co-regulating transcription factors from expression time-series by Bayesian model comparison.

Titsias MK, Honkela A, Lawrence ND, Rattray M. Titsias MK, et al. Among authors: honkela a. BMC Syst Biol. 2012 May 30;6:53. doi: 10.1186/1752-0509-6-53. BMC Syst Biol. 2012. PMID: 22647244 Free PMC article.

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