20062020

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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)
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)

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)
357 Downloads (Pure)
2018

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)
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)
108 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)
205 Downloads (Pure)

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)

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
41 Citations (Scopus)
70 Downloads (Pure)

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)

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

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)

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

243 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)
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)
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

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

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)