• PL 68 (Pietari Kalmin katu 5)

    00014

    Finland

  • Finland

20102019
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Publications 2010 2019

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2019

Representation transfer for differentially private drug sensitivity prediction

Niinimäki, T., Heikkilä, M. A., Honkela, A. & Kaski, S., 5 Jul 2019, In : Bioinformatics. 35, 14, p. i218-i224 7 p.

Research output: Contribution to journalArticleScientificpeer-review

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Seasonal Variation in Genome-Wide DNA Methylation Patterns and the Onset of Seasonal Timing of Reproduction in Great Tits

Viitaniemi, H. M., Verhagen, I., Visser, M. E., Honkela, A., van Oers, K. & Husby, A., Mar 2019, In : Genome Biology and Evolution. 11, 3, p. 970-983 14 p.

Research output: Contribution to journalArticleScientificpeer-review

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2018

Efficient differentially private learning improves drug sensitivity prediction

Honkela, A., Das, M., Nieminen, A., Dikmen, O. & Kaski, S., 6 Feb 2018, In : Biology Direct. 13, 12 p., 1.

Research output: Contribution to journalArticleScientificpeer-review

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

Topa, H. & Honkela, A., 4 Oct 2018, In : BMC Bioinformatics. 19, 6 p., 367.

Research output: Contribution to journalArticleScientificpeer-review

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2017

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., 28 Sep 2017, In : PeerJ. 5, 23 p., 3742.

Research output: Contribution to journalArticleScientificpeer-review

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2016

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

Topa, H. & Honkela, A., 15 Jun 2016, In : Bioinformatics. 32, 12, p. 147-155 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Bayesian identification of bacterial strains from sequencing data

Sankar, A., Malone, B. M., Bayliss, S. C., Pascoe, B., Méric, G., Hitchings, M. D., Sheppard, S. K., Feil, E. J., Corander, J. I. & Honkela, A. J. H., 25 Aug 2016, In : Microbial Genomics. 2, 8, 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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On the inconsistency of ℓ1-penalised sparse precision matrix estimation

Heinävaara, O., Leppä-Aho, J., Corander, J. & Honkela, A., 13 Dec 2016, In : BMC Bioinformatics. 17, Suppl 16, p. 99-107 9 p.

Research output: Contribution to journalArticleScientificpeer-review

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RNA Production Delays Shape Transcriptional Response Dynamics

Honkela, A. J. H. & Rattray, M., 25 May 2016, In : Cell Systems. 2, 5, p. 291 1 p.

Research output: Contribution to journalArticleScientific

Open Access

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

Lees, J. A., Vehkala, M., Välimäki, N., Harris, S. R., Chewapreecha, C., Croucher, N. J., Marttinen, P., Davies, M. R., Steer, A. C., Tong, S. Y. C., Honkela, A., Parkhill, J., Bentley, S. & Corander, J., 16 Sep 2016, In : Nature Communications. 7, 8 p., 12797.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2015

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

Hensman, J., Papastamoulis, P., Glaus, P., Honkela, A. J. H. & Rattray, M., 15 Dec 2015, In : Bioinformatics. 31, 24, p. 3881-3889 9 p.

Research output: Contribution to journalArticleScientificpeer-review

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

Topa, H., Jonas, A., Kofler, R., Kosiol, C. & Honkela, A., 1 Jun 2015, In : Bioinformatics. 31, 11, p. 1762-1770 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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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, H. G., Reid, G., Lawrence, N. D. & Rattray, M., 20 Oct 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 42, p. 13115-13120 6 p.

Research output: Contribution to journalArticleScientificpeer-review

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

Uziela, K. & Honkela, A., 12 May 2015, In : PLoS One. 10, 5, 18 p., 0126545.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2014

A community effort to assess and improve drug sensitivity prediction algorithms

Costello, J. C., Heiser, L. M., Georgii, E., Gonen, M., Menden, M. P., Wang, N. J., Bansal, M., Ammad-ud-din, M., Hintsanen, P., Khan, S. A., Mpindi, J-P., Kallioniemi, O., Honkela, A., Aittokallio, T., Wennerberg, K., Collins, J. J., Gallahan, D., Singer, D., Saez-Rodriguez, J., Kaski, S. & 3 others, Gray, J. W., Stolovitzky, G. & NCI DREAM Community, Dec 2014, In : Nature Biotechnology. 32, 12, p. 1202-U57 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Exploration and retrieval of whole-metagenome sequencing samples

Seth, S., Valimaki, N., Kaski, S. & Honkela, A., 1 Sep 2014, In : Bioinformatics. 30, 17, p. 2471-2479 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data

wa Maina, C., Honkela, A., Matarese, F., Grote, K., Stunnenberg, H. G., Reid, G., Lawrence, N. D. & Rattray, M., May 2014, In : PLoS Computational Biology. 10, 5, 17 p., e1003598.

Research output: Contribution to journalArticleScientificpeer-review

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2012

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

Glaus, P., Honkela, A. & Rattray, M., 2012, In : Bioinformatics. 28, 13, p. 1721-1728 8 p.

Research output: Contribution to journalArticleScientificpeer-review

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

Titsias, M. K., Honkela, A., Lawrence, N. D. & Rattray, M., 30 May 2012, In : BMC Systems Biology. 6, 21 p., 53.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2011

Missing-Feature Reconstruction With a Bounded Nonlinear State-Space Model

Remes, U., Palomaki, K. J., Raiko, T., Honkela, A. & Kurimo, M., 2011, In : IEEE Signal Processing Letters. 18, 10, p. 563-566 4 p.

Research output: Contribution to journalArticleScientificpeer-review

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

Honkela, A., Gao, P., Ropponen, J., Rattray, M. & Lawrence, N. D., 2011, In : Bioinformatics. 27, 7, p. 1026-1027 2 p.

Research output: Contribution to journalArticleScientificpeer-review

2010

Approximate Riemannian Conjugate Gradient Learning for Fixed-Form Variational Bayes

Honkela, A., Raiko, T., Kuusela, M., Tornio, M. & Karhunen, J., 2010, In : Journal of Machine Learning Research. 11, p. 3235-3268 34 p.

Research output: Contribution to journalArticleScientificpeer-review

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

Honkela, A., Girardot, C., Gustafson, E. H., Liu, Y-H., Furlong, E. E. M., Lawrence, N. D. & Rattray, M., 2010, In : Proceedings of the National Academy of Sciences of the United States of America. 107, p. 7793-7798 6 p.

Research output: Contribution to journalArticleScientificpeer-review