20062020

Research output per year

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Research Output

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)
90 Downloads (Pure)

Improved Small Molecule Identification through Learning Combinations of Kernel Regression Models

Brouard, C., Basse, A., d'Alche-Buc, F. & Rousu, J., Aug 2019, In : METABOLITES. 9, 8, 14 p., 160.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
1 Citation (Scopus)
121 Downloads (Pure)

Large-Scale Sparse Kernel Canonical Correlation Analysis

Uurtio, V., Bhadra, S. & Rousu, J., 2019, 36th International Conference on Machine Learning, ICML 2019. p. 6383-6391 9 p. (Proceedings of Machine Learning Research; vol. 97).

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

Open Access
File
10 Downloads (Pure)

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information

Dührkop, K., Fleischauer, M., Ludwig, M., Aksenov, A. A., Melnik, A. V., Meusel, M., Dorrestein, P. C., Rousu, J. & Böcker, S., 1 Apr 2019, In : Nature Methods. 16, 4, p. 299-302 4 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
71 Citations (Scopus)
356 Downloads (Pure)
2018

Analysis of fluxomic experiments with principal metabolic flux mode analysis

Bhadra, S. & Rousu, J., 1 Jan 2018, Methods in Molecular Biology. Mamitsuka, H. (ed.). p. 141-161 21 p. (Methods in Molecular Biology; vol. 1807).

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

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)
82 Downloads (Pure)

Liquid-chromatography retention order prediction for metabolite identification

Bach, E., Szedmak, S., Brouard, C., Boecker, S. & Rousu, J., 1 Sep 2018, In : Bioinformatics. 34, 17, p. 875-883 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
14 Citations (Scopus)
63 Downloads (Pure)

Principal metabolic flux mode analysis

Bhadra, S., Blomberg, P., Castillo, S. & Rousu, J., 2018, In : Bioinformatics. 34, 14, p. 2409-2417

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
137 Downloads (Pure)

Sparse Non-linear CCA through Hilbert-Schmidt Independence Criterion

Uurtio, V., Bhadra, S. & Rousu, J., 2018, 2018 IEEE International Conference on Data Mining, ICDM 2018. IEEE, p. 1278-1283 6 p. 8594981

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

Open Access
File
1 Citation (Scopus)
182 Downloads (Pure)
2017

A Tutorial on Canonical Correlation Methods

Uurtio, V., Monteiro, J. M., Kandola, J., Shawe-Taylor, J., Fernandez-Reyes, D. & Rousu, J., 2017, In : ACM COMPUTING SURVEYS. 50, 6, p. 1-33 95.

Research output: Contribution to journalArticleScientificpeer-review

CamOptimus: a tool for exploiting complex adaptive evolution to optimize experiments and processes in biotechnology

Cankorur-Cetinkaya, A., Dias, J. M. L., Kludas, J., Slater, N. K. H., Rousu, J., Oliver, S. G. & Dikicioglu, D., 2017, In : MICROBIOLOGY. 163, 6, p. 829-839 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
7 Citations (Scopus)
41 Downloads (Pure)

Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors

Cichonska, A., Ravikumar, B., Parri, E., Timonen, S., Pahikkala, T., Airola, A., Wennerberg, K., Rousu, J. & Aittokallio, T., 1 Aug 2017, In : PLoS computational biology. 13, 8, p. 1-28 e1005678.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
27 Citations (Scopus)
130 Downloads (Pure)

Critical Assessment of Small Molecule Identification 2016: automated methods

Schymanski, E. L., Ruttkies, C., Krauss, M., Brouard, C., Kind, T., Dührkop, K., Allen, F., Vaniya, A., Verdegem, D., Böcker, S., Rousu, J., Shen, H., Tsugawa, H., Sajed, T., Fiehn, O., Ghesquière, B. & Neumann, S., 27 Mar 2017, In : JOURNAL OF CHEMINFORMATICS. 9, 1, 22.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
60 Citations (Scopus)
107 Downloads (Pure)

Magnitude-preserving ranking for structured outputs

Brouard, C., Bach, E., Böcker, S. & Rousu, J., 1 Jan 2017, In : Journal of Machine Learning Research. 77, p. 407-422 16 p.

Research output: Contribution to journalConference articleScientificpeer-review

6 Citations (Scopus)

Magnitude-Preserving Ranking for Structured Outputs

Brouard, C., Bach, E., Böcker, S. & Rousu, J., 3 Nov 2017, Proceedings of the Ninth Asian Conference on Machine Learning. Zhang, M-L. & Noh, Y-K. (eds.). p. 407-422 16 p. (Proceedings of Machine Learning Research; vol. 77).

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

Open Access
File
9 Downloads (Pure)

Multi-view kernel completion

Bhadra, S., Kaski, S. & Rousu, J., May 2017, In : Machine Learning. 106, 5, p. 713–739

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
14 Citations (Scopus)
204 Downloads (Pure)

Predicting Protein Producibility In Filamentous Fungi

Dykstra, K., Rousu, J. & Arvas, M., 2017, p. 1-18.

Research output: Working paperProfessional

Principal Metabolic Flux Mode Analysis

Bhadra, S., Blomberg, P., Castillo, S. & Rousu, J., 2017, In : bioRxiv. p. 163055 7 p.

Research output: Contribution to journalArticleScientific

Open Access
2016

Computational Metabolomics (Dagstuhl Seminar 15492)

Böcker, S., Rousu, J. & Schymanski, E., 2016, In : DAGSTUHL REPORTS. 5, 11, p. 180-192 13 p.

Research output: Contribution to journalArticleScientific

Open Access
File
69 Downloads (Pure)

Fast metabolite identification with Input Output Kernel Regression

Brouard, C., Shen, H., Dührkop, K., d'Alché-Buc, F., Böcker, S. & Rousu, J., 15 Jun 2016, In : Bioinformatics. 32, 12, p. 28-36

Research output: Contribution to journalArticleScientificpeer-review

29 Citations (Scopus)

Generating data to improve protein stability prediction

Heinonen, M., Jokinen, E., Kaski, S., Rousu, J. & Lähdesmäki, H., 2016, Patent No. Provisional US 62/361511

Research output: Patent

Machine learning of protein interactions in fungal secretory pathways

Kludas, J., Arvas, M., Castillo, S., Pakula, T., Oja, M., Brouard, C., Jäntti, J., Penttilä, M. & Rousu, J., 1 Jul 2016, In : PloS one. 11, 7, p. 1-20 20 p., e0159302.

Research output: Contribution to journalArticleScientificpeer-review

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

metaCCA: summary statistics-based multivariate meta-analysis of genome-wide association studies using canonical correlation analysis

Cichonska, A., Rousu, J., Marttinen, P., Kangas, A. J., Soininen, P., Lehtimaki, T., Raitakari, O., Jarvelin, M-R., Salomaa, V., Ala-Korpela, M., Ripatti, S. & Pirinen, M., 1 Jul 2016, In : Bioinformatics. 32, 13, p. 1981-1989 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
40 Citations (Scopus)
70 Downloads (Pure)

Non-Stationary Gaussian Process Regression with Hamiltonian Monte Carlo

Heinonen, M., Mannerström, H., Rousu, J., Kaski, S. & Lähdesmäki, H., 2016, Proceedings of the 19th International Conference on Artificial Intelligence and Statistics: JMLR: W&CP. JMLR, p. 732-740 9 p. ( JMLR: Workshop and Conference Proceedings; vol. 51).

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

Profiling persistent tubercule bacilli from patient sputa during therapy predicts early drug efficacy

Honeyborne, I., McHugh, T. D., Kuittinen, I., Cichonska, A., Evangelopoulos, D., Ronacher, K., van Helden, P. D., Gillespie, S. H., Fernandez-Reyes, D., Walzl, G., Rousu, J., Butcher, P. D. & Waddell, S. J., 7 Apr 2016, In : BMC MEDICINE. 14, 1, p. 1-13 68.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
17 Citations (Scopus)
127 Downloads (Pure)

Selected proceedings of Machine Learning in Systems Biology: MLSB 2016

van Dijk, A. D. J., Lähdesmäki, H., de Ridder, D. & Rousu, J., 13 Dec 2016, In : BMC Bioinformatics. 17, Supplement 16, 2 p.

Research output: Contribution to journalEditorialScientific

Open Access
File
3 Citations (Scopus)
55 Downloads (Pure)

Selected proceedings of Machine Learning in Systems Biology: MLSB 2016

van Dijk, A. D. J., Lähdesmäki, H., de Ridder, D. & Rousu, J., Dec 2016, In : BMC Bioinformatics. 17

Research output: Contribution to journalSpecial issueScientificpeer-review

Soft Kernel Target Alignment for Two-stage Multiple Kernel Learning

Shen, H., Szedmak, S., Brouard, C. & Rousu, J., Oct 2016, Discovery Science: 19th International Conference, DS 2016, Bari, Italy, October 19–21, 2016, Proceedings. Calders, T., Ceci, M. & Malerba, D. (eds.). 1 ed. Springer International Publishing, Vol. 9956. p. 427-441 (Lecture Notes in Artificial Intelligence; vol. 9956).

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

Synthetic transcription amplifier system for orthogonal control of gene expression in saccharomyces cerevisiae

Rantasalo, A., Czeizler, E., Virtanen, R., Rousu, J., Lähdesmäki, H., Penttilä, M., Jäntti, J. & Mojzita, D., 1 Feb 2016, In : PloS one. 11, 2, p. 1-19 e0148320.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
16 Citations (Scopus)
234 Downloads (Pure)
2015

Canonical Correlation Methods for Exploring Microbe-Environment Interactions in Deep Subsurface

Uurtio, V., Bomberg, M., Nybo, K., Itävaara, M. & Rousu, J., 2015, 18th International Conference on Discovery Science, Banff, Canada, October 4-6, 2015. Springer International Publishing, p. 299-307

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

2 Citations (Scopus)

Identification of drug candidates and repurposing opportunities through compound-target interaction networks

Cichonska, A., Rousu, J. & Aittokallio, T., 2015, In : EXPERT OPINION ON DRUG DISCOVERY. 10, 12, p. 1333-1345

Research output: Contribution to journalReview ArticleScientificpeer-review

26 Citations (Scopus)

Meat Processing Plant Microbiome and Contamination Patterns of Cold-Tolerant Bacteria Causing Food Safety and Spoilage Risks in the Manufacture of Vacuum-Packaged Cooked Sausages

Hultman, J., Rahkila, R., Ali, J., Rousu, J. & Bjorkroth, K. J., 2015, In : Applied and Environmental Microbiology. 81, 20, p. 7088-7097

Research output: Contribution to journalArticleScientificpeer-review

60 Citations (Scopus)

Multilabel Classification through Random Graph Ensembles

Su, H. & Rousu, J., 2015, In : Machine Learning. 99, 2, p. 231-256 26 p.

Research output: Contribution to journalArticleScientificpeer-review

7 Citations (Scopus)

Optimization of environmental parameters for improving recombinant protein production by the host Komagataella (Pichia) pastoris

Cankorur-Cetinkaya, A., Dikicioglu, D., Kludas, J., Rousu, J. & Oliver, S. G., 2015, p. pp. S148-S148.

Research output: Working paperProfessional

Search engine targets metabolites using MS

Rousu, J., Dec 2015, In : TRAC-TRENDS IN ANALYTICAL CHEMISTRY. 74, 1 p.

Research output: Contribution to journalComment/debateScientific

Searching molecular structure databases with tandem mass spectra using CSI:FingerID

Dührkop, K., Shen, H., Meusel, M., Rousu, J. & Böcker, S., 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 41, p. 12580-12585

Research output: Contribution to journalArticleScientificpeer-review

240 Citations (Scopus)
2014

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species

Pitkänen, E., Jouhten, P., Hou, J., Fahad Syed, M., Blomberg, P., Kludas, J., Oja, M., Holm, L., Penttilä, M. & Rousu, J., 2014, In : PLoS computational biology. 10, 2, p. 1-12 e1003465.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
39 Citations (Scopus)
168 Downloads (Pure)

Metabolite identification through multiple kernel learning on fragmentation trees

Shen, H., Dührkop, K., Böcker, S. & Rousu, J., 2014, In : Bioinformatics. 30, 12, p. pp. i157-i164

Research output: Contribution to journalArticleScientificpeer-review

57 Citations (Scopus)

Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks

Marchand, M., Su, H., Morvant, E., Rousu, J. & Shawe-Taylor, J., 2014, Annual Conference on Neural Information Processing Systems, Montreal, Quebec, Canada, December 8 - December 13, 2014. p. 873-881

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

3 Citations (Scopus)

Structured Prediction of Network Response

Su, H., Gionis, A. & Rousu, J., 2014, International Conference on Machine Learning, Beijing, China, June 21 - June 26, 2014. p. 442-450

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

2013

Biomarker Discovery by Sparse Canonical Correlation Analysis of Complex Clinical Phenotypes of Tuberculosis and Malaria

Rousu, J., Agranoff, D. D., Sodeinde, O., Shawe-Taylor, J. & Fernandez-Reyes, D., 2013, In : PLoS computational biology. 9, 4, p. 1-10 1003018.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
12 Citations (Scopus)
142 Downloads (Pure)

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
139 Downloads (Pure)

Multilabel Classification through Random Graph Ensembles

Su, H. & Rousu, J., 2013, 5th Asian Conference on Machine Learning, Canberra, Australia, November 11 - November 15, 2013. p. 404-418

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

3 Citations (Scopus)
2012

Efficient Path Kernels for Reaction Function Prediction

Heinonen, M., Välimäki, N., Mäkinen, V. & Rousu, J., 2012, Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms. p. 202-207

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

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

84 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

2010

Multilabel classification of drug-like molecules via max-margin conditional random fields

Su, H., Heinonen, M. & Rousu, J., 2010, Proceedings of The Fifth European Workshop on Probabilistic Graphical Models (PGM-2010): 13-15 September, 2010, Helsinki, Finland. Myllymäki, P., Roos, T. & Jaakkola, T. (eds.). HIIT, p. 265-272 (HIIT Publications; vol. 2010, no. 2).

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

Structured output prediction of anti-cancer drug activity

Su, H., Heinonen, M. & Rousu, J., 2010, Pattern Recognition in Bioinformatics: 5th IAPR International Conference, PRIB 2010, Nijmegen, The Netherlands, September 22-24, 2010. Proceedings. Dijkstra, T. M. H., Tsivtsivadze, E., Marchiori, E. & Heskes, T. (eds.). Springer Verlag, p. 38-49 ( Lecture Notes in Computer Science; vol. 6282).

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

2007

Probabilistic modeling and machine learning in structural and systems biology

Kaski, S., Rousu, J. & Ukkonen, E., 2007, In : BMC Bioinformatics. 8 (Suppl2), p. S1/1-2

Research output: Contribution to journalArticleScientificpeer-review

1 Citation (Scopus)