20062020

Research output per year

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2019

Bayesian metabolic flux analysis reveals intracellular flux couplings

Heinonen, M., Osmala, M., Mannerström, H., Wallenius, J., Kaski, S., Rousu, J. & Lähdesmäki, H., 15 Jul 2019, In : Bioinformatics. 35, 14, p. i548-i557 btz315.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
1 Citation (Scopus)
86 Downloads (Pure)
2018

Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein–Protein Binding Affinity upon Mutation

Barlow, K., Conchuir, S., Thompson, S., Suresh, P., Lucas, J., Heinonen, M. & Kortemme, T., 31 May 2018, In : Journal of Physical Chemistry B. 122, 21, p. 5389-5399 11 p.

Research output: Contribution to journalArticleScientificpeer-review

23 Citations (Scopus)

Learning with multiple pairwise kernels for drug bioactivity prediction

Cichonska, A., Pahikkala, T., Szedmak, S., Julkunen, H., Airola, A., Heinonen, M., Aittokallio, T. & Rousu, J., 1 Jul 2018, In : Bioinformatics. 34, 13, p. i509-i518

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
4 Citations (Scopus)
75 Downloads (Pure)

MGPfusion: Predicting protein stability changes with Gaussian process kernel learning and data fusion

Jokinen, E., Heinonen, M. & Lähdesmäki, H., 1 Jul 2018, In : Bioinformatics. 34, 13, p. i274-i283

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
6 Citations (Scopus)
69 Downloads (Pure)

Temporal clustering analysis of endothelial cell gene expression following exposure to a conventional radiotherapy dose fraction using Gaussian process clustering

Heinonen, M., Milliat, F., Benadjaoud, M. A., François, A., Buard, V., Tarlet, G., D'Alché-Buc, F. & Guipaud, O., 1 Oct 2018, In : PloS one. 13, 10, p. 1-31 e0204960.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
133 Downloads (Pure)
2016

Genome wide analysis of protein production load in Trichoderma reesei

Pakula, T. M., Nygren, H., Barth, D., Heinonen, M., Castillo, S., Penttilä, M. & Arvas, M., 28 Jun 2016, In : Biotechnology for Biofuels. 9, 1, p. 1-26 132.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
12 Citations (Scopus)
148 Downloads (Pure)
2015

Detecting time periods of differential gene expression using Gaussian processes: an application to endothelial cells exposed to radiotherapy dose fraction

Heinonen, M., Guipaud, O., Milliat, F., Buard, V., Micheau, B., Tarlet, G., Benderitter, M., Zehraoui, F. & d'Alche-Buc, F., 1 Mar 2015, In : Bioinformatics. 31, 5, p. 728-735 8 p.

Research output: Contribution to journalArticleScientificpeer-review

2013

Metabolite Identification through Machine Learning- Tackling CASMI Challenge Using FingerID

Shen, H., Zamboni, N., Heinonen, M. & Rousu, J., 2013, In : METABOLITES. 3, 2, p. 484-505

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
136 Downloads (Pure)
2012

Metabolite identification and molecular fingerprint prediction through machine learning

Heinonen, M., Shen, H., Zamboni, N. & Rousu, J., 2012, In : Bioinformatics. 28, 18, p. 2333-2341

Research output: Contribution to journalArticleScientificpeer-review

82 Citations (Scopus)
2011

Computing Atom Mappings for Biochemical Reactions without Subgraph Isomorphism

Heinonen, M., Lappalainen, S., Mielikäinen, T. & Rousu, J., Jan 2011, In : JOURNAL OF COMPUTATIONAL BIOLOGY. 18, 1, p. 43-58 16 p.

Research output: Contribution to journalArticleScientificpeer-review

2008

FiD: a software for ab initio structural identification of product ions from tandem mass spectrometric data

Heinonen, M., Rantanen, A., Mielikaeinen, T., Kokkonen, J., Kiuru, J., Ketola, R. A. & Rousu, J., Oct 2008, In : Rapid Communications in Mass Spectrometry. 22, 19, p. 3043-3052 10 p.

Research output: Contribution to journalArticleScientificpeer-review