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Publications 2010 2018

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

Open Access
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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

Open Access
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Identifying Bacterial Strains from Sequencing Data

Mäklin, T., Corander, J. & Honkela, A., 2018, Data Mining for Systems Biology: Methods and Protocols. Mamitsuka, H. (ed.). 2 ed. New York, NY: Humana press, p. 1-7 7 p. (Methods in Molecular Biology; vol. 1807).

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

Learning rate adaptation for differentially private stochastic gradient descent

Koskela, A. H. & Honkela, A. J. H., 8 Dec 2018.

Research output: Conference materialsPosterResearchpeer-review

2017

Differentially private Bayesian learning on distributed data

Heikkila, M., Lagerspetz, E., Kaski, S., Shimizu, K., Tarkoma, S. & Honkela, A., 2017, Advances in Neural Information Processing Systems 30 (NIPS 2017). Guyon, I., Luxburg, U. V., Bengio, S., Wallach, H., Fergus, R., Vishwanathan, S. & Garnett, R. (eds.). NEURAL INFORMATION PROCESSING SYSTEMS (NIPS), Vol. 30. 10 p. (Advances in Neural Information Processing Systems; vol. 30).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Open Access
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Differentially Private Variational Inference for Non-conjugate Models

Jälkö, J., Dikmen, O. & Honkela, A., 2017, Uncertainty in Artificial Intelligence 2017: Proceedings of the 33rd Conference, UAI 2017 . Elidan, G. & Kersting, K. (eds.). The Association for Uncertainty in Artificial Intelligence, 10 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Open Access
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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

Open Access
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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

Open Access
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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 modelling of multiple short time series

Topa, H. & Honkela, A. J. H., 2015, ESANN 2015: Proceedings of the 23rd European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning. ESANN, p. 83-88 6 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

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 othersGray, 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

Open Access
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2013

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

Honkela, A., Rattray, M. & Lawrence, N. D., 2013, Data Mining for Systems Biology: Methods and Protocols. Mamitsuka, H., DeLisi, C. & Kanehisa, M. (eds.). Humana Press, p. 59-67 9 p. (Methods in Molecular Biology; vol. 939).

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

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

A Generative Approach for Image-Based Modeling of Tumor Growth

Menze, B. H., Van Leemput, K., Honkela, A., Konukoglu, E., Weber, M-A., Ayache, N. & Golland, P., 2011, Information Processing in Medical Imaging: 22nd International Conference, IPMI 2011, Kloster Irsee, Germany, July 3-8, 2011. Proceedings. Székely, G. & Hahn, H. K. (eds.). Springer-Verlag, p. 735-747 13 p. (Lecture Notes in Computer Science; vol. 6801).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Enemmän vai laadukkaammin

Honkela, A., 2011, Kirjeitä nuorelle tutkijalle: kannanottoja tutkijan arjesta. Paso, M. (ed.). Helsinki: Suomalainen Tiedeakatemia, p. 38-42 5 p. (Suomalaisen Tiedeakatemian kannanottoja; vol. 3).

Research output: Chapter in Book/Report/Conference proceedingChapterGeneral public

Gaussian Process Inference for Differential Equation Models of Transcriptional Regulation

Lawrence, N., Rattray, M., Honkela, A. & Titsias, M., 2011, Handbook of Statistical Systems Biology. Stumpf, M. P. H., Balding, D. J. & Girolami, M. (eds.). John Wiley & Sons Ltd. , p. 376-394 19 p.

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

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