Simulation of microarray data with realistic characteristics. - Matti Nykter; Tommi Aho; Miika Ahdesmäki; Pekka Ruusuvuori; Antti Lehmussola; Olli Yli-Harja (BMC Bioinform., 2006)

Signal processing methods and information approach to systems biology. - Matti Nykter (2006)

Computational Methods for Estimation of Cell Cycle Phase Distributions of Yeast Cells. - Antti Niemistö; Matti Nykter; Tommi Aho; Henna Jalovaara; Kalle Marjanen; Miika Ahdesmäki; Pekka Ruusuvuori; Mikko Tiainen; Marja-Leena Linne; Olli Yli-Harja (EURASIP J. Bioinform. Syst. Biol., 2007)

Set-based complexity and biological information - David J. Galas; Matti Nykter; Gregory W. Carter; Nathan D. Price 001; Ilya Shmulevich (CoRR, 2008)

Biological information as set-based complexity. - David J. Galas; Matti Nykter; Gregory W. Carter; Nathan D. Price 001; Ilya Shmulevich (IEEE Trans. Inf. Theory, 2010)

Information Diversity in Structure and Dynamics of Simulated Neuronal Networks. - Tuomo Mäki-Marttunen; Jugoslava Acimovic; Matti Nykter; Juha Kesseli; Keijo Ruohonen; Olli Yli-Harja; Marja-Leena Linne (Frontiers Comput. Neurosci., 2011)

Characterization of aberrant pathways across human cancers. - Antti Ylipää; Olli Yli-Harja; Wei Zhang 011; Matti Nykter (BMC Syst. Biol., 2013)

Mapping dynamical states to structural classes for Boolean networks using a classification algorithm. - Septimia Sârbu; Ilya Shmulevich; Olli Yli-Harja; Matti Nykter; Juha Kesseli (EUSIPCO, 2015)

Benchmarking of algorithms for 3D tissue reconstruction. - Kimmo Kartasalo; Leena Latonen; Tapio Visakorpi; Matti Nykter; Pekka Ruusuvuori (ICIP, 2016)

Dual Structured Convolutional Neural Network with Feature Augmentation for Quantitative Characterization of Tissue Histology. - Mira Valkonen; Kimmo Kartasalo; Kaisa Liimatainen; Matti Nykter; Leena Latonen; Pekka Ruusuvuori (ICCV Workshops, 2017)

Segmentum: a tool for copy number analysis of cancer genomes. - Ebrahim Afyounian; Matti Annala; Matti Nykter (BMC Bioinform., 2017)

Comparative analysis of tissue reconstruction algorithms for 3D histology. - Kimmo Kartasalo; Leena Latonen; Jorma Vihinen; Tapio Visakorpi; Matti Nykter; Pekka Ruusuvuori (Bioinform., 2018)

Cytokeratin-Supervised Deep Learning for Automatic Recognition of Epithelial Cells in Breast Cancers Stained for ER, PR, and Ki-67. - Mira Valkonen; Jorma Isola; Onni Ylinen; Ville Muhonen; Anna Saxlin; Teemu Tolonen; Matti Nykter; Pekka Ruusuvuori (IEEE Trans. Medical Imaging, 2020)

ECCB2024: The 23rd European Conference on Computational Biology. - Anu Kukkonen-Macchi; Sampsa Hautaniemi; Katharina F. Heil; Merja Heinäniemi; Lars Juhl Jensen; Sini Junttila; Lukas Käll; Asta Laiho; Peter Maccallum; Matti Nykter; Bengt Persson; Tomi Suomi; et al. (Bioinform., 2024)