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Items: 1 to 20 of 23

1.

GPrank: an R package for detecting dynamic elements from genome-wide time series.

Topa H, Honkela A.

BMC Bioinformatics. 2018 Oct 4;19(1):367. doi: 10.1186/s12859-018-2370-4.

2.

Identifying Bacterial Strains from Sequencing Data.

Mäklin T, Corander J, Honkela A.

Methods Mol Biol. 2018;1807:1-7. doi: 10.1007/978-1-4939-8561-6_1.

PMID:
30030799
3.

Efficient differentially private learning improves drug sensitivity prediction.

Honkela A, Das M, Nieminen A, Dikmen O, Kaski S.

Biol Direct. 2018 Feb 6;13(1):1. doi: 10.1186/s13062-017-0203-4.

4.

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.

PeerJ. 2017 Sep 28;5:e3742. doi: 10.7717/peerj.3742. eCollection 2017.

5.

Bayesian identification of bacterial strains from sequencing data.

Sankar A, Malone B, Bayliss SC, Pascoe B, Méric G, Hitchings MD, Sheppard SK, Feil EJ, Corander J, Honkela A.

Microb Genom. 2016 Aug 25;2(8):e000075. doi: 10.1099/mgen.0.000075. eCollection 2016 Aug.

6.

On the inconsistency of ℓ 1-penalised sparse precision matrix estimation.

Heinävaara O, Leppä-Aho J, Corander J, Honkela A.

BMC Bioinformatics. 2016 Dec 13;17(Suppl 16):448. doi: 10.1186/s12859-016-1309-x.

7.

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes.

Lees JA, Vehkala M, Välimäki N, Harris SR, Chewapreecha C, Croucher NJ, Marttinen P, Davies MR, Steer AC, Tong SY, Honkela A, Parkhill J, Bentley SD, Corander J.

Nat Commun. 2016 Sep 16;7:12797. doi: 10.1038/ncomms12797.

8.

Analysis of differential splicing suggests different modes of short-term splicing regulation.

Topa H, Honkela A.

Bioinformatics. 2016 Jun 15;32(12):i147-i155. doi: 10.1093/bioinformatics/btw283.

9.

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.

Proc Natl Acad Sci U S A. 2015 Oct 20;112(42):13115-20. doi: 10.1073/pnas.1420404112. Epub 2015 Oct 5.

10.

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

Hensman J, Papastamoulis P, Glaus P, Honkela A, Rattray M.

Bioinformatics. 2015 Dec 15;31(24):3881-9. doi: 10.1093/bioinformatics/btv483. Epub 2015 Aug 26.

11.

Probe Region Expression Estimation for RNA-Seq Data for Improved Microarray Comparability.

Uziela K, Honkela A.

PLoS One. 2015 May 12;10(5):e0126545. doi: 10.1371/journal.pone.0126545. eCollection 2015.

12.

Gaussian process test for high-throughput sequencing time series: application to experimental evolution.

Topa H, Jónás Á, Kofler R, Kosiol C, Honkela A.

Bioinformatics. 2015 Jun 1;31(11):1762-70. doi: 10.1093/bioinformatics/btv014. Epub 2015 Jan 21.

13.

A community effort to assess and improve drug sensitivity prediction algorithms.

Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K; NCI DREAM Community, Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G.

Nat Biotechnol. 2014 Dec;32(12):1202-12. doi: 10.1038/nbt.2877. Epub 2014 Jun 1.

14.

Exploration and retrieval of whole-metagenome sequencing samples.

Seth S, Välimäki N, Kaski S, Honkela A.

Bioinformatics. 2014 Sep 1;30(17):2471-9. doi: 10.1093/bioinformatics/btu340. Epub 2014 May 19.

15.

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.

PLoS Comput Biol. 2014 May 15;10(5):e1003598. doi: 10.1371/journal.pcbi.1003598. eCollection 2014 May.

16.

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

Honkela A, Rattray M, Lawrence ND.

Methods Mol Biol. 2013;939:59-67. doi: 10.1007/978-1-62703-107-3_6.

PMID:
23192541
17.

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

Titsias MK, Honkela A, Lawrence ND, Rattray M.

BMC Syst Biol. 2012 May 30;6:53. doi: 10.1186/1752-0509-6-53.

18.

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

Glaus P, Honkela A, Rattray M.

Bioinformatics. 2012 Jul 1;28(13):1721-8. doi: 10.1093/bioinformatics/bts260. Epub 2012 May 3.

19.

A generative approach for image-based modeling of tumor growth.

Menze BH, Van Leemput K, Honkela A, Konukoglu E, Weber MA, Ayache N, Golland P.

Inf Process Med Imaging. 2011;22:735-47.

20.

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

Honkela A, Gao P, Ropponen J, Rattray M, Lawrence ND.

Bioinformatics. 2011 Apr 1;27(7):1026-7. doi: 10.1093/bioinformatics/btr057. Epub 2011 Feb 7.

PMID:
21300702

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