Juho Rousu

Professor

Research outputs

  1. 2019
  2. Published

    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 journalArticle

  3. Published

    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 journalArticle

  4. Published

    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 journalArticle

  5. Published

    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

  6. 2018
  7. Published

    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 journalArticle

  8. Published

    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 journalArticle

  9. Published

    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

  10. Published

    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 journalArticle

  11. Published

    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

  12. 2017
  13. Published

    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

  14. Published

    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 journalArticle

  15. Published

    Multi-view kernel completion

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

    Research output: Contribution to journalArticle

  16. Published

    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. & 7 others, 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 journalArticle

  17. Published

    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 article

  18. Published

    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 journalArticle

  19. Published

    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 journalArticle

  20. Published

    Predicting Protein Producibility In Filamentous Fungi

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

    Research output: Working paperProfessional

  21. Published

    Principal Metabolic Flux Mode Analysis

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

    Research output: Contribution to journalArticle

  22. 2016
  23. Published

    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 journalEditorial

  24. Published

    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 issue

  25. Published

    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

  26. Published

    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 journalArticle

  27. Published

    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. & 2 others, Ripatti, S. & Pirinen, M., 1 Jul 2016, In : Bioinformatics. 32, 13, p. 1981-1989 9 p.

    Research output: Contribution to journalArticle

  28. Published

    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 journalArticle

  29. Published

    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. & 3 others, Rousu, J., Butcher, P. D. & Waddell, S. J., 7 Apr 2016, In : BMC MEDICINE. 14, 1, p. 1-13 68.

    Research output: Contribution to journalArticle

  30. Published

    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 journalArticle

  31. Published

    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 journalArticle

  32. Published

    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

  33. Published

    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

  34. 2015
  35. Published

    Search engine targets metabolites using MS

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

    Research output: Contribution to journalComment/debate

  36. Published

    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

  37. Published

    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 Article

  38. Published
  39. Published

    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 journalArticle

  40. Published

    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

  41. Published

    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 journalArticle

  42. 2014
  43. Published

    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 journalArticle

  44. Published

    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 journalArticle

  45. Published

    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

  46. Published

    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

  47. 2013
  48. Published

    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 journalArticle

  49. Published

    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 journalArticle

  50. Published

    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

  51. 2012
  52. Published

    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

  53. Published

    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 journalArticle

  54. 2011
  55. Published

    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 journalArticle

  56. 2010
  57. Published

    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

  58. Published

    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

  59. 2008
  60. Published

    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 journalArticle

  61. 2007
  62. Published

    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 journalArticle

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