RousuAalto University

Juho Rousu

Associate professor, Information and Computer Science, Department of Computer Science

What do you do?

What do you do?

 

  • Vice-head of Department of Computer Science (Research matters)
  • Vice-Chair of Board of Aalto Health Platform
  • Steering group of Helsinki institute for Information Technology HIIT
  • Leader of Kernel Methods, Pattern Analysis and Computational Metabolomics (KEPACO) research group in Aalto ICS department & HIIT
  • Activities
    • LiF - Living Factories. Tekes strategic opening grant 2014-2016.
    • MIDAS - Metabolite Identification through Algorithms and Statistical Learning. Acadamy of Finland grant (2013-2017)
    • D4Health - Data-driven Decision support for Digital Health. Academy of Finland grant (2016-2018)
    • Recent program committees: AISTATS'16, NIPS'16, MLSB'16, ECML/PKDD'16
  • Selection of my publications can be found on the KEPACO group pages
  • My profiles on ResearchGate and  Linkedin

Where do you come from?

Where do you come from=
  • Main previous professional appointments
    • Professor (pro tem) University of Helsinki 
    • Marie Curie Fellow, Royal Holloway University of London 
    • VTT Technical Research Centre of Finland 

Keywords

Contact information

Preferred contact method
email first.last@aalto.fi
Work street address
Konemiehentie 2 (PO Box 15400)
00076 Aalto
Espoo
Finland
Work phone
+358 50 4151702

Publications

Peer-reviewed scientific articles

Journal article-refereed, Original research

Multi-view kernel completion

Bhadra, Sahely; Kaski, Samuel; Rousu, Juho 

2017 

MACHINE LEARNING 

ISSN: 1573-0565 

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

Cankorur-Cetinkaya, Ayca; Dias, Joao M. L.; Kludas, Jana; Slater, Nigel K. H.; Rousu, Juho; Oliver, Stephen G.; Dikicioglu, Duygu 

2017 

MICROBIOLOGY 

ISSN: 1350-0872 

Critical Assessment of Small Molecule Identification 2016 automated methods

Schymanski, Emma L.; Ruttkies, Christoph; Krauss, Martin; Brouard, Céline; Kind, Tobias; Dührkop, Kai; Allen, Felicity; Vaniya, Arpana; Verdegem, Dries; Böcker, Sebastian; Rousu, Juho; Shen, Huibin; Tsugawa, Hiroshi; Sajed, Tanvir; Fiehn, Oliver; Ghesquière, Bart; Neumann, Steffen 

2017 

JOURNAL OF CHEMINFORMATICS 

ISSN: 1758-2946 

Fast metabolite identification with Input Output Kernel Regression

Brouard, Celine; Shen, Huibin; Dührkop, Kai; d'Alché-Buc, Florence; Böcker, Sebastian; Rousu, Juho 

2016 

BIOINFORMATICS 

ISSN: 1367-4803 

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

Cichonska, Anna; Rousu, Juho; Marttinen, Pekka; Kangas, Antti J.; Soininen, Pasi; Lehtimaki, Terho; Raitakari, Olli; Jarvelin, Marjo-Riitta; Salomaa, Veikko; Ala-Korpela, Mika; Ripatti, Samuli; Pirinen, Matti 

2016 

BIOINFORMATICS 

ISSN: 1367-4803 

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

Honeyborne, Isobella; McHugh, Timothy D.; Kuittinen, Iitu; Cichonska, Anna; Evangelopoulos, Dimitrios; Ronacher, Katharina; van Helden, Paul D.; Gillespie, Stephen H.; Fernandez-Reyes, Delmiro; Walzl, Gerhard; Rousu, Juho; Butcher, Philip D.; Waddell, Simon J. 

2016 

BMC MEDICINE 

ISSN: 1741-7015 

Machine learning of protein interactions in fungal secretory pathways

Kludas, Jana; Arvas, Mikko; Castillo, Sandra; Pakula, Tiina; Oja, Merja; Brouard, Céline; Jäntti, Jussi; Penttilä, Merja; Rousu, Juho 

2016 

PLOS ONE 

ISSN: 1932-6203 

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

Rantasalo, Anssi; Czeizler, Elena; Virtanen, Riitta; Rousu, Juho; Lähdesmäki, Harri; Penttilä, Merja; Jäntti, Jussi; Mojzita, Dominik 

2016 

PLOS ONE 

ISSN: 1932-6203 

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

Dührkop, Kai; Shen, Huibin; Meusel, Marvin; Rousu, Juho; Böcker, Sebastian 

2015 

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 

ISSN: 0027-8424 

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, Jenni; Rahkila, Riitta; Ali, Javeria; Rousu, Juho; Bjorkroth, K.Johanna 

2015 

APPLIED AND ENVIRONMENTAL MICROBIOLOGY 

ISSN: 0099-2240 

Multilabel Classification through Random Graph Ensembles.

Su, Hongyu; Rousu, Juho 

2015 

MACHINE LEARNING 

ISSN: 0885-6125 

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

Pitkänen, Esa; Jouhten, Paula; Hou, Jian; Fahad Syed, Muhammad; Blomberg, Peter; Kludas, Jana; Oja, Merja; Holm, Liisa; Penttilä, Merja; Rousu, Juho 

2014 

PLOS COMPUTATIONAL BIOLOGY 

ISSN: 1553-734X 

Metabolite identification through multiple kernel learning on fragmentation trees

Shen, Huibin; Dührkop, Kai; Böcker, Sebastian; Rousu, Juho 

2014 

BIOINFORMATICS 

ISSN: 1367-4803 

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

Rousu, Juho; Agranoff, Daniel D.; Sodeinde, Olugbemiro; Shawe-Taylor, John; Fernandez-Reyes, Delmiro 

2013 

PLOS COMPUTATIONAL BIOLOGY 

ISSN: 1553-734X 

Metabolite Identification through Machine Learning- Tackling CASMI Challenge Using FingerID

Shen, Huibin; Zamboni, Nicola; Heinonen, Markus; Rousu, Juho 

2013 

METABOLITES 

Metabolite identification and molecular fingerprint prediction through machine learning

Heinonen, M.; Shen, H.; Zamboni, N.; Rousu, J. 

2012 

BIOINFORMATICS 

ISSN: 1367-4803 

Computing Atom Mappings for Biochemical Reactions without Subgraph Isomorphism

Heinonen, Markus; Lappalainen, Sampsa; Mielikäinen, Taneli; Rousu, Juho 

2011 

JOURNAL OF COMPUTATIONAL BIOLOGY 

ISSN: 1066-5277 

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

Heinonen, Markus; Rantanen, Ari; Mielikaeinen, Taneli; Kokkonen, Juha; Kiuru, Jari; Ketola, Raimo A.; Rousu, Juho 

2008 

RAPID COMMUNICATIONS IN MASS SPECTROMETRY 

ISSN: 0951-4198 

Probabilistic modeling and machine learning in structural and systems biology

Kaski, Samuel; Rousu, Juho; Ukkonen, Esko 

2007 

BMC BIOINFORMATICS 

Review article, Literature review, Systematic review

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

Cichonska, Anna; Rousu, Juho; Aittokallio, Tero 

2015 

EXPERT OPINION ON DRUG DISCOVERY 

ISSN: 1746-0441 

Conference proceedings

Non-Stationary Gaussian Process Regression with Hamiltonian Monte Carlo

Heinonen, Markus; Mannerström, Henrik; Rousu, Juho; Kaski, Samuel; Lähdesmäki, Harri 

2016 

JMLR: Workshop and Conference Proceedings 

JMLR 

ISSN: 1938-7228 

Soft Kernel Target Alignment for Two-stage Multiple Kernel Learning

Shen, Huibin; Szedmak, Sandor; Brouard, Celine; Rousu, Juho 

2016 

Lecture Notes in Artificial Intelligence 

Springer International Publishing 

ISBN: 978-3-319-46306-3 

ISSN: 0302-9743 

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

Uurtio, Viivi; Bomberg, Malin; Nybo, Kristian; Itävaara, Merja; Rousu, Juho 

2015 

Springer International Publishing 

ISBN: 978-3-319-24281-1 

ISSN: 0302-9743 

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

Marchand, Mario; Su, Hongyu; Morvant, Emilie; Rousu, Juho; Shawe-Taylor, John 

2014 

ISSN: 1049-5258 

Structured Prediction of Network Response

Su, Hongyu; Gionis, Aristides; Rousu, Juho 

2014 

ISSN: 1938-7228 

Multilabel Classification through Random Graph Ensembles

Su, Hongyu; Rousu, Juho 

2013 

ISSN: 1938-7228 

Efficient Path Kernels for Reaction Function Prediction

Heinonen, Markus; Välimäki, Niko; Mäkinen, Veli; Rousu, Juho 

2012 

Non-refereed scientific articles

Unrefereed journal articles

Computational Metabolomics (Dagstuhl Seminar 15492)

Böcker, Sebastian; Rousu, Juho; Schymanski, Emma 

2016 

DAGSTUHL REPORTS 

ISSN: 2192-5283 

Selected proceedings of Machine Learning in Systems Biology MLSB 2016

van Dijk, Aalt D J; Lähdesmäki, Harri; de Ridder, Dick; Rousu, Juho 

2016 

BMC BIOINFORMATICS 

ISSN: 1471-2105 

Scientific books (monographs)

Book (editor)

Probabilistic Modeling and Machine Learning in Structural and Systems Biology

Rousu, Juho; Kaski, Samuel; Ukkonen, Esko 

2006 

University of Helsinki 

Publications intended for professional communities

Published development or research report

Predicting Protein Producibility In Filamentous Fungi

Dykstra, Karmen; Rousu, Juho; Arvas, Mikko 

2017 

Cold Spring Harbor Labs Journals 

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

Cankorur-Cetinkaya, Ayca; Dikicioglu, Duygu; Kludas, Jana; Rousu, Juho; Oliver, Stephen G. 

2015 

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