Juho Rousu

Peer-reviewed scientific articles

Journal article-refereed, Original research

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 review

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 proceedings

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 articles

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, 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 report

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

Patent

Generating data to improve protein stability prediction

Heinonen, Markus; Jokinen, Emmi; Kaski, Samuel; Rousu, Juho; Lähdesmäki, Harri

2016