Tracking metastable states to free-energy global minima. - Bruce W. Church; Matej Oresic; David Shalloway (Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, 1995)

Data integration and visualization system for enabling conceptual biology. - Peddinti V. Gopalacharyulu; Erno Lindfors; Catherine Bounsaythip; Teemu Kivioja; Laxman Yetukuri; Jaakko Hollmén; Matej Oresic (ISMB (Supplement of Bioinformatics), 2005)

Processing methods for differential analysis of LC/MS profile data. - Mikko Katajamaa; Matej Oresic (BMC Bioinform., 2005)

MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data. - Mikko Katajamaa; Jarkko Miettinen; Matej Oresic (Bioinform., 2006)

Exploring the lipoprotein composition using Bayesian regression on serum lipidomic profiles. - Marko Sysi-Aho; Aki Vehtari; Vidya R. Velagapudi; Jukka Westerbacka; Laxman Yetukuri; Robert Bergholm; Marja-Riitta Taskinen; Hannele Yki-Järvinen; Matej Oresic (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process. - Laura Elo; Henna Järvenpää; Matej Oresic; Riitta Lahesmaa; Tero Aittokallio (Bioinform., 2007)

Normalization method for metabolomics data using optimal selection of multiple internal standards. - Marko Sysi-Aho; Mikko Katajamaa; Laxman Yetukuri; Matej Oresic (BMC Bioinform., 2007)

Bioinformatics strategies for lipidomics analysis: characterization of obesity related hepatic steatosis. - Laxman Yetukuri; Mikko Katajamaa; Gema Medina-Gómez; Tuulikki Seppänen-Laakso; Antonio Vidal-Puig; Matej Oresic (BMC Syst. Biol., 2007)

megNet®: Visualization and Modelling Environment for Translational Medicine. - Matej Oresic; Jyrki Lötjönen; Catherine Bounsaythip (ERCIM News, 2007)

An integrative approach for biological data mining and visualisation. - Peddinti V. Gopalacharyulu; Erno Lindfors; Jarkko Miettinen; Catherine Bounsaythip; Matej Oresic (Int. J. Data Min. Bioinform., 2008)

Two-way analysis of high-dimensional collinear data. - Ilkka Huopaniemi; Tommi Suvitaival; Janne Nikkilä; Matej Oresic; Samuel Kaski (Data Min. Knowl. Discov., 2009)

Searching for Linear Dependencies between Heart Magnetic Resonance Images and Lipid Profiles. - Marko Sysi-Aho; Juha Koikkalainen; Jyrki Lötjönen; Tuulikki Seppänen-Laakso; Hans Söderlund; Tiina Heliö; Matej Oresic (Algorithms and Applications, 2010)

METAtarget - Extracting Key Enzymes of Metabolic Regulation from Highthroughput Metabolomics Data using KEGG REACTION Information. - Jan Budczies; Carsten Denkert; Berit M. Müller; Scarlet F. Brockmöller; Manfred Dietel; Jules L. Griffin; Matej Oresic; Oliver Fiehn (GCB, 2010)

Graphical Multi-way Models. - Ilkka Huopaniemi; Tommi Suvitaival; Matej Oresic; Samuel Kaski (ECML/PKDD (1), 2010)

Multivariate multi-way analysis of multi-source data. - Ilkka Huopaniemi; Tommi Suvitaival; Janne Nikkilä; Matej Oresic; Samuel Kaski (Bioinform., 2010)

MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. - Tomás Pluskal; Sandra Castillo; Alejandro Villar-Briones; Matej Oresic (BMC Bioinform., 2010)

Cross-Species Translation of Multi-way Biomarkers. - Tommi Suvitaival; Ilkka Huopaniemi; Matej Oresic; Samuel Kaski (ICANN (1), 2011)

MPEA - metabolite pathway enrichment analysis. - Matti Kankainen; Peddinti V. Gopalacharyulu; Liisa Holm; Matej Oresic (Bioinform., 2011)

Compartmentation of glycogen metabolism revealed from 13C isotopologue distributions. - Igor Marín de Mas; Vitaly A. Selivanov; Silvia Marin; Josep Roca; Matej Oresic; Loranne Agius; Marta Cascante (BMC Syst. Biol., 2011)

Matching samples of multiple views. - Abhishek Tripathi; Arto Klami; Matej Oresic; Samuel Kaski (Data Min. Knowl. Discov., 2011)

Metabolic Regulation in Progression to Autoimmune Diabetes. - Marko Sysi-Aho; Andrey Ermolov; Peddinti V. Gopalacharyulu; Abhishek Tripathi; Tuulikki Seppänen-Laakso; Johanna Maukonen; Ismo Mattila; Suvi T. Ruohonen; Laura Vähätalo; Laxman Yetukuri; Taina Härkönen; Erno Lindfors; et al. (PLoS Comput. Biol., 2011)

Integration of transcription and flux data reveals molecular paths associated with differences in oxygen-dependent phenotypes of Saccharomyces cerevisiae. - Erno Lindfors; Paula Jouhten; Merja Oja; Eija Rintala; Matej Oresic; Merja Penttilä (BMC Syst. Biol., 2014)

Self-organization and missing values in SOM and GTM. - Tommi Vatanen; Maria Osmala; Tapani Raiko; Krista Lagus; Marko Sysi-Aho; Matej Oresic; Timo Honkela; Harri Lähdesmäki (Neurocomputing, 2015)

Deep learning meets metabolomics: a methodological perspective. - Partho Sen; Santosh Lamichhane; Vivek Bhakta Mathema; Aidan J. McGlinchey; Alex M. Dickens; Sakda Khoomrung; Matej Oresic (Briefings Bioinform., 2021)