Juho Rousu
Associate professor, Information and Computer Science at Aalto University School of Business
Schools
- Aalto University School of Business
Links
Biography
Aalto University School of Business
- 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
BACKGROUND
- Main previous professional appointments
- Professor (pro tem) University of Helsinki
- Marie Curie Fellow, Royal Holloway University of London
- VTT Technical Research Centre of Finland
Peer-reviewed scientific articles
Journal article-refereed, Original researchMulti-view kernel completion
Bhadra, Sahely; Kaski, Samuel; Rousu, Juho2017 in MACHINE LEARNING (Springer Netherlands)ISSN: 1573-0565CamOptimus 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, Duygu2017 in MICROBIOLOGY (Microbiology Society)ISSN: 1350-0872Computational-experimental approach to drug-target interaction mapping A case study on kinase inhibitors
Cichonska, Anna; Ravikumar, Balaguru; Parri, Elina; Timonen, Sanna; Pahikkala, Tapio; Airola, Antti; Wennerberg, Krister; Rousu, Juho; Aittokallio, Tero2017 in PLOS COMPUTATIONAL BIOLOGY (Public Library of Science)ISSN: 1553-734XCritical 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, Steffen2017 in JOURNAL OF CHEMINFORMATICS (SPRINGER)ISSN: 1758-2946Fast metabolite identification with Input Output Kernel Regression
Brouard, Celine; Shen, Huibin; Dührkop, Kai; d'Alché-Buc, Florence; Böcker, Sebastian; Rousu, Juho2016 in BIOINFORMATICS (OXFORD UNIV PRESS INC)ISSN: 1367-4803metaCCA 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, Matti2016 in BIOINFORMATICS (OXFORD UNIV PRESS INC)ISSN: 1367-4803Profiling 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 in BMC MEDICINE (BioMed Central)ISSN: 1741-7015Machine 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, Juho2016 in PLOS ONE (PUBLIC LIBRARY SCIENCE)ISSN: 1932-6203Synthetic 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, Dominik2016 in PLOS ONE (PUBLIC LIBRARY SCIENCE)ISSN: 1932-6203Searching molecular structure databases with tandem mass spectra using CSI:FingerID
Dührkop, Kai; Shen, Huibin; Meusel, Marvin; Rousu, Juho; Böcker, Sebastian2015 in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (NATL ACAD SCIENCES)ISSN: 0027-8424Meat 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.Johanna2015 in APPLIED AND ENVIRONMENTAL MICROBIOLOGY (AMER SOC MICROBIOLOGY)ISSN: 0099-2240Multilabel Classification through Random Graph Ensembles.
Su, Hongyu; Rousu, Juho2015 in MACHINE LEARNING (Springer Netherlands)ISSN: 0885-6125Comparative 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, Juho2014 in PLOS COMPUTATIONAL BIOLOGY (Public Library of Science)ISSN: 1553-734XMetabolite identification through multiple kernel learning on fragmentation trees
Shen, Huibin; Dührkop, Kai; Böcker, Sebastian; Rousu, Juho2014 in BIOINFORMATICS (OXFORD UNIV PRESS INC)ISSN: 1367-4803Biomarker 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, Delmiro2013 in PLOS COMPUTATIONAL BIOLOGY (Public Library of Science)ISSN: 1553-734XMetabolite Identification through Machine Learning- Tackling CASMI Challenge Using FingerID
Shen, Huibin; Zamboni, Nicola; Heinonen, Markus; Rousu, Juho2013 in METABOLITES (Public Library of Science)Metabolite identification and molecular fingerprint prediction through machine learning
Heinonen, M.; Shen, H.; Zamboni, N.; Rousu, J.2012 in BIOINFORMATICS (OXFORD UNIV PRESS INC)ISSN: 1367-4803Computing Atom Mappings for Biochemical Reactions without Subgraph Isomorphism
Heinonen, Markus; Lappalainen, Sampsa; Mielikäinen, Taneli; Rousu, Juho2011 in JOURNAL OF COMPUTATIONAL BIOLOGY (Mary Ann Liebert Inc.)ISSN: 1066-5277FiD 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, Juho2008 in RAPID COMMUNICATIONS IN MASS SPECTROMETRY (JOHN WILEY & SONS LTD)ISSN: 0951-4198Probabilistic modeling and machine learning in structural and systems biology
Kaski, Samuel; Rousu, Juho; Ukkonen, Esko2007 in BMC BIOINFORMATICS (BioMed Central)
Multi-view kernel completion
Bhadra, Sahely; Kaski, Samuel; Rousu, Juho
2017 in MACHINE LEARNING (Springer Netherlands)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 in MICROBIOLOGY (Microbiology Society)ISSN: 1350-0872
Computational-experimental approach to drug-target interaction mapping A case study on kinase inhibitors
Cichonska, Anna; Ravikumar, Balaguru; Parri, Elina; Timonen, Sanna; Pahikkala, Tapio; Airola, Antti; Wennerberg, Krister; Rousu, Juho; Aittokallio, Tero
2017 in PLOS COMPUTATIONAL BIOLOGY (Public Library of Science)ISSN: 1553-734X
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 in JOURNAL OF CHEMINFORMATICS (SPRINGER)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 in BIOINFORMATICS (OXFORD UNIV PRESS INC)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 in BIOINFORMATICS (OXFORD UNIV PRESS INC)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 in BMC MEDICINE (BioMed Central)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 in PLOS ONE (PUBLIC LIBRARY SCIENCE)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 in PLOS ONE (PUBLIC LIBRARY SCIENCE)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 in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (NATL ACAD SCIENCES)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 in APPLIED AND ENVIRONMENTAL MICROBIOLOGY (AMER SOC MICROBIOLOGY)ISSN: 0099-2240
Multilabel Classification through Random Graph Ensembles.
Su, Hongyu; Rousu, Juho
2015 in MACHINE LEARNING (Springer Netherlands)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 in PLOS COMPUTATIONAL BIOLOGY (Public Library of Science)ISSN: 1553-734X
Metabolite identification through multiple kernel learning on fragmentation trees
Shen, Huibin; Dührkop, Kai; Böcker, Sebastian; Rousu, Juho
2014 in BIOINFORMATICS (OXFORD UNIV PRESS INC)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 in PLOS COMPUTATIONAL BIOLOGY (Public Library of Science)ISSN: 1553-734X
Metabolite Identification through Machine Learning- Tackling CASMI Challenge Using FingerID
Shen, Huibin; Zamboni, Nicola; Heinonen, Markus; Rousu, Juho
2013 in METABOLITES (Public Library of Science)Metabolite identification and molecular fingerprint prediction through machine learning
Heinonen, M.; Shen, H.; Zamboni, N.; Rousu, J.
2012 in BIOINFORMATICS (OXFORD UNIV PRESS INC)ISSN: 1367-4803
Computing Atom Mappings for Biochemical Reactions without Subgraph Isomorphism
Heinonen, Markus; Lappalainen, Sampsa; Mielikäinen, Taneli; Rousu, Juho
2011 in JOURNAL OF COMPUTATIONAL BIOLOGY (Mary Ann Liebert Inc.)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 in RAPID COMMUNICATIONS IN MASS SPECTROMETRY (JOHN WILEY & SONS LTD)ISSN: 0951-4198
Probabilistic modeling and machine learning in structural and systems biology
Kaski, Samuel; Rousu, Juho; Ukkonen, Esko
2007 in BMC BIOINFORMATICS (BioMed Central)Review article, Literature review, Systematic reviewIdentification of drug candidates and repurposing opportunities through compound-target interaction networks
Cichonska, Anna; Rousu, Juho; Aittokallio, Tero2015 in EXPERT OPINION ON DRUG DISCOVERY (Informa Healthcare)ISSN: 1746-0441
Identification of drug candidates and repurposing opportunities through compound-target interaction networks
Cichonska, Anna; Rousu, Juho; Aittokallio, Tero
2015 in EXPERT OPINION ON DRUG DISCOVERY (Informa Healthcare)ISSN: 1746-0441
Conference proceedingsNon-Stationary Gaussian Process Regression with Hamiltonian Monte Carlo
Heinonen, Markus; Mannerström, Henrik; Rousu, Juho; Kaski, Samuel; Lähdesmäki, Harri2016 in JMLR: Workshop and Conference Proceedings (JMLR)ISSN: 1938-7228Soft Kernel Target Alignment for Two-stage Multiple Kernel Learning
Shen, Huibin; Szedmak, Sandor; Brouard, Celine; Rousu, Juho2016 in Lecture Notes in Artificial Intelligence (Springer International Publishing)ISBN: 978-3-319-46306-3ISSN: 0302-9743Canonical Correlation Methods for Exploring Microbe-Environment Interactions in Deep Subsurface
Uurtio, Viivi; Bomberg, Malin; Nybo, Kristian; Itävaara, Merja; Rousu, Juho2015 ISBN: 978-3-319-24281-1ISSN: 0302-9743Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks
Marchand, Mario; Su, Hongyu; Morvant, Emilie; Rousu, Juho; Shawe-Taylor, John2014 ISSN: 1049-5258Structured Prediction of Network Response
Su, Hongyu; Gionis, Aristides; Rousu, Juho2014 ISSN: 1938-7228Multilabel Classification through Random Graph Ensembles
Su, Hongyu; Rousu, Juho2013 ISSN: 1938-7228Efficient Path Kernels for Reaction Function Prediction
Heinonen, Markus; Välimäki, Niko; Mäkinen, Veli; Rousu, Juho2012 Multilabel classification of drug-like molecules via max-margin conditional random fields
Su, Hongyu; Heinonen, Markus; Rousu, Juho2010 in HIIT Publications (HIIT)ISBN: 978-952-60-3314-3ISSN: 1458-946XStructured output prediction of anti-cancer drug activity
Su, Hongyu; Heinonen, Markus; Rousu, Juho2010 in Lecture Notes in Computer Science (Springer-Verlag)ISBN: 978-3-642-16000-4ISSN: 0302-9743Ab Initio prediction of molecular fragments from tandem mass spectrometry data
Heinonen, Markus; Rantanen, Ari; Mielikäinen, Taneli; Pitkänen, Esa; Kokkonen, Juha T.; Rousu, Juho2006 in Lecture Notes in Informatics (LNI) (Gesellschaft fur Informatik (GI))ISBN: 978-3-88579-177-5
Non-Stationary Gaussian Process Regression with Hamiltonian Monte Carlo
Heinonen, Markus; Mannerström, Henrik; Rousu, Juho; Kaski, Samuel; Lähdesmäki, Harri
2016 in 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 in 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 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 Multilabel classification of drug-like molecules via max-margin conditional random fields
Su, Hongyu; Heinonen, Markus; Rousu, Juho
2010 in HIIT Publications (HIIT)ISBN: 978-952-60-3314-3
ISSN: 1458-946X
Structured output prediction of anti-cancer drug activity
Su, Hongyu; Heinonen, Markus; Rousu, Juho
2010 in Lecture Notes in Computer Science (Springer-Verlag)ISBN: 978-3-642-16000-4
ISSN: 0302-9743
Ab Initio prediction of molecular fragments from tandem mass spectrometry data
Heinonen, Markus; Rantanen, Ari; Mielikäinen, Taneli; Pitkänen, Esa; Kokkonen, Juha T.; Rousu, Juho
2006 in Lecture Notes in Informatics (LNI) (Gesellschaft fur Informatik (GI))ISBN: 978-3-88579-177-5
Non-refereed scientific articles
Unrefereed journal articlesComputational Metabolomics (Dagstuhl Seminar 15492)
Böcker, Sebastian; Rousu, Juho; Schymanski, Emma2016 in DAGSTUHL REPORTS (Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik)ISSN: 2192-5283Selected proceedings of Machine Learning in Systems Biology MLSB 2016
van Dijk, Aalt D J; Lähdesmäki, Harri; de Ridder, Dick; Rousu, Juho2016 in BMC BIOINFORMATICS (BioMed Central)ISSN: 1471-2105
Computational Metabolomics (Dagstuhl Seminar 15492)
Böcker, Sebastian; Rousu, Juho; Schymanski, Emma
2016 in DAGSTUHL REPORTS (Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik)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 in BMC BIOINFORMATICS (BioMed Central)ISSN: 1471-2105
Scientific books (monographs)
Book (editor)Selected proceedings of Machine Learning in Systems Biology MLSB 2016
van Dijk, Aalt D J; Lähdesmäki, Harri; de Ridder, Dick; Rousu, Juho2016 in BMC BIOINFORMATICS (BioMed Central)ISSN: 1471-2105Probabilistic Modeling and Machine Learning in Structural and Systems Biology
Rousu, Juho; Kaski, Samuel; Ukkonen, Esko2006
Selected proceedings of Machine Learning in Systems Biology MLSB 2016
van Dijk, Aalt D J; Lähdesmäki, Harri; de Ridder, Dick; Rousu, Juho
2016 in BMC BIOINFORMATICS (BioMed Central)ISSN: 1471-2105
Probabilistic Modeling and Machine Learning in Structural and Systems Biology
Rousu, Juho; Kaski, Samuel; Ukkonen, Esko
2006 Publications intended for professional communities
Published development or research reportPredicting Protein Producibility In Filamentous Fungi
Dykstra, Karmen; Rousu, Juho; Arvas, Mikko2017 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
Predicting Protein Producibility In Filamentous Fungi
Dykstra, Karmen; Rousu, Juho; Arvas, Mikko
2017 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 Patents and invention disclosures
PatentGenerating data to improve protein stability prediction
Heinonen, Markus; Jokinen, Emmi; Kaski, Samuel; Rousu, Juho; Lähdesmäki, Harri2016
Generating data to improve protein stability prediction
Heinonen, Markus; Jokinen, Emmi; Kaski, Samuel; Rousu, Juho; Lähdesmäki, Harri
2016 Videos
Juho Rousu: "Predicting structured data"
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