## Workpage of Antti Honkela
Assistant Professor (tenure track), Department of Mathematics and Statistics
and Department of Public Health, University of Helsinki My research interests include Bayesian machine learning and computational systems biology. I am interested in modelling nonlinear dynamical systems, especially modelling transcriptional regulation, and analysis of RNA-sequencing data and alternative splicing. I am an action editor for the Journal of Machine Learning Research, Machine Learning Open Source Software section, and an associate editor for Statistical Applications in Genetics and Molecular Biology.
## News- I have started as an assistant professor (tenure track) of statistics at the Department of Mathematics and Statistics and the Department of Public Health at the University of Helsinki.
- New paper "Bayesian identification of bacterial strains from sequencing data" has been published in Microbial Genomics.
- New paper "Analysis of differential splicing suggests different modes of short-term splicing regulation" has been published in Bioinformatics (ISMB 2016).
- New paper "Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays" has been published in PNAS.
- New paper "Fast and accurate approximate inference of transcript expression from RNA-seq data" has been published in Bioinformatics.
- Our recent work on Genome-wide modelling of transcription kinetics reveals patterns of RNA processing delays will be presented as a late-breaking research talk at ISMB/ECCB 2015.
- I am co-organising the Privacy-aware computational genomics 2015 (PRIVAGEN 2015) workshop in Tokyo in September 2015.
- I am co-organising the ICML 2015 Workshop on Machine Learning Open Source Software: Open Ecosystems
- I am organising the 25th Annual MASAMB Workshop on Mathematical and Statistical Aspects of Molecular Biology in Helsinki in April 2015.
- New paper "Gaussian process test for high-throughput sequencing time series: application to experimental evolution" has been published in Bioinformatics.
- New paper "Exploration and retrieval of whole-metagenome sequencing samples" has been published in Bioinformatics.
- New paper "Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data" has been published in PLoS Computational Biology.
- I am co-organising the Workshop on Machine Learning Open Source Software 2013: Towards Open Workflows at NIPS 2013
- I started a 5 year Academy Research Fellowship funded by the Academy of Finland at the University of Helsinki in September 2012.
- Our joint HIIT-FIMM team "TeamFIN" won the NCI-DREAM Drug Sensitivity Prediction Challenge in DREAM7.
- New paper "Identifying targets of multiple co-regulating transcription factors from expression time-series by Bayesian model comparison" was published in BMC Systems Biology.
- New paper "Identifying differentially expressed transcripts from RNA-seq data with biological variation" was published in Bioinformatics. The BitSeq software package implementing the method is also available.
## Research group## PostdocOnur Dikmen ## PhD students
Hande Topa ## Contact information
Room A344 at Department of Computer Science, Exactum,
University of Helsinki ## Mailing address:
Helsinki Institute for Information Technology HIIT ## Software- My group's software releases on GitHub.
- BitSeq software for transcript-level expression and differential expression estimation from RNA-sequencing data is available as a standalone C++ package and in BitSeq Bioconductor package.
- The tigre package implementing the transcription factor target ranking method from our recent PNAS paper is available in Bioconductor. A Matlab implementation used to produce the results reported in the paper is also available.
- tigreBrowser is a web-based browser for displaying and ranking genomic modelling results. It allows easy viewing, sorting and filtering of visualisations of models from tigre or other tools.
- Older free software tools I have created are available on the pages of the Bayes and IVGA groups.
## Teaching**University of Helsinki:**- Autumn 2016
- 58316301 Seminar on Probabilistic Programming
- 582746 Modelling and Analysis in Bioinformatics
- Autumn 2015
- 582746 Modelling and Analysis in Bioinformatics
- Autumn 2014
- 58314301 Seminar in Probabilistic Models for Big Data
- Spring 2014
- 582637 Project in Probabilistic Models
- Spring 2013
- 582637 Project in Probabilistic Models
- Spring 2012
- 582637 Project in Probabilistic Models
- Spring 2011
- 582637 Project in Probabilistic Models
**Helsinki University of Technology:**- Spring 2009
- T-61.6070 Special Course in Bioinformatics I: Learning and Inference in Dynamic Models of Biological Networks
- Autumn 2008
- T-61.5110 Modelling of biological networks
- 2006-2007
- Scientific coordinator of the International Master's Programme in Machine Learning and Data Mining - Macadamia
- Spring 2007
- T-61.152 Informaatiotekniikan seminaari: tiedonhaku (Seminar in Computer and Information Science: Information retrieval)
- Autumn 2006
- T-61.6010 Special Course in Computer and Information Science I: Gaussian Processes for Machine Learning
- Spring 2006
- T-61.152 Informaatiotekniikan seminaari: ydinfunktiomenetelmät (Seminar in Computer and Information Science: Kernel methods)
- 2005-2006
- Coordinator for the lab of Computer and Information Science for the department of Computer Science and Engineering B.Sc. seminar (Kandidaattiseminaari)
- Autumn 2004
- T-61.182 Information Theory and Machine Learning
- Autumn 2001
- T-61.181 Independent Component Analysis
## PublicationsGoogle ScholarPubmed ## Pre-prints
A. Sankar, B. Malone, S. Bayliss, B. Pascoe, G. Méric, M.D. Hitchings, S.K. Sheppard, E.J. Feil, J. Corander and A. Honkela
B. Rakitsch, C. Lippert, H. Topa, K. Borgwardt, A. Honkela and O. Stegle.
H. Topa and A. Honkela. ## Journal articles
A. Honkela, J. Peltonen, H. Topa, I. Charapitsa, F. Matarese, K. Grote,
H.G. Stunnenberg, G. Reid, N.D. Lawrence and M. Rattray.
J. Hensman, P. Papastamoulis, P. Glaus, A. Honkela, and M. Rattray.
K. Uziela and A. Honkela.
H. Topa, Á Jónás, R. Kofler, C. Kosiol, and A. Honkela.
J. C. Costello, L. M. Heiser, E. Georgii, M. Gönen, M. P. Menden,
N. J. Wang, M. Bansal, M. Ammad-ud-din, P. Hintsanen, S. A. Khan,
J-P. Mpindi, O. Kallioniemi, A. Honkela, T. Aittokallio, K. Wennerberg,
NCI DREAM Community, J. J. Collins, D. Gallahan, D. Singer,
J. Saez-Rodriguez, S. Kaski, J. W. Gray, and G. Stolovitzky.
S. Seth, N. Välimäki, S. Kaski, and A. Honkela.
C. wa Maina, A. Honkela, F. Matarese, K. Grote, H. G. Stunnenberg,
G. Reid, N. D. Lawrence, and M. Rattray.
M. Titsias
P. Glaus, A. Honkela
U. Remes, K. J. Palomäki, T. Raiko, A. Honkela, and M. Kurimo.
A. Honkela, P. Gao, J. Ropponen, M. Rattray, N. D. Lawrence.
A. Honkela
A. Honkela, C. Girardot, E. H. Gustafson, Y.-H. Liu, E. E. M. Furlong,
N. D. Lawrence and M. Rattray.
P. Gao, A. Honkela, M. Rattray, and N. D. Lawrence.
A. Honkela, J. Seppä, and E. Alhoniemi.
A. Honkela, H. Valpola, A. Ilin, and J. Karhunen.
E. Alhoniemi, A. Honkela, K. Lagus, J. Seppä, P. Wagner, and
H. Valpola.
A. Honkela and H. Valpola.
A. Honkela, H. Valpola and J. Karhunen.
H. Valpola, E. Oja, A. Ilin, A. Honkela and J. Karhunen. ## Book chapters
N. Lawrence, M. Rattray, A. Honkela, and M. Titsias.
H. Lappalainen and A. Honkela. ## Conference papers
B. H. Menze, K. Van Leemput, A. Honkela, E. Konukoglu,
M. A. Weber, N. Ayache, and P. Golland.
V. Peltola and A. Honkela.
A. Honkela, M. Milo, M. Holley, M. Rattray, and N. D. Lawrence.
M. Kuusela, T. Raiko, A. Honkela, and J. Karhunen.
A. Honkela, M. Tornio, T. Raiko, and J. Karhunen.
A. Honkela, J. Seppä, and E. Alhoniemi.
M. Tornio, A. Honkela, and J. Karhunen. J. Nikkilä, A. Honkela, and S. Kaski.
T. Raiko, M. Tornio, A. Honkela and J. Karhunen.
M. Harva, T. Raiko, A. Honkela, H. Valpola and J. Karhunen.
K. Lagus, E. Alhoniemi, J. Seppä, A. Honkela and P. Wagner.
A. Honkela, T. Östman, R. Vigário.
A. Honkela and H. Valpola.
A. Ilin and A. Honkela.
A. Honkela, S. Harmeling, L. Lundqvist and H. Valpola.
A. Honkela.
V. Siivola and A. Honkela.
A. Honkela and H. Valpola.
A. Honkela.
H. Valpola, A. Honkela, and J. Karhunen.
H. Valpola, A. Honkela, and J. Karhunen.
A. Honkela and J. Karhunen.
H. Valpola, X. Giannakopoulos, A. Honkela, and J. Karhunen.
H. Lappalainen, A. Honkela, X. Giannakopoulos, and J. Karhunen. ## Conference abstracts and presentationsA. Honkela, M. Tornio, and T. Raiko. A. Honkela, M. Harva, T. Raiko, H. Valpola, and J. Karhunen. A. Honkela. ## Theses
A. Honkela.
A. Honkela. ## Technical reports
H. Valpola and A. Honkela. This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder. ## LinksMy personal home page (in Finnish) |