Analysis of the properties of median and weighted median filters using threshold logic and stack filter representation. - Olli Yli-Harja; Jaakko Astola; Yrjö Neuvo (IEEE Trans. Signal Process., 1991)

Formula for the joint distribution of stack filters. - Olli Yli-Harja (IEEE Signal Process. Lett., 1994)

State reduction of recursive median filters. - Olli P. Yli-Harja; J. Andrew Bangham; Richard W. Harvey (Electronic Imaging: Nonlinear Image Processing, 1999)

Correlation properties of cascaded recursive median filters. - Olli Yli-Harja; J. Andrew Bangham; Richard W. Harvey; Richard V. Aldridge (NSIP, 1999)

Graph-based smoothing of class data with applications in musical key finding. - Olli Yli-Harja; Ilya Shmulevich; Kjell Lemström (NSIP, 1999)

Output distributions of recursive stack filters. - Ilya Shmulevich; Olli Yli-Harja; Karen O. Egiazarian; Jaakko Astola (IEEE Signal Process. Lett., 1999)

Reduction factors in finite automata with application to nonlinear filters. - Antti Niemistö; Olli Yli-Harja; Antti Valmari; Pertti Koivisto; Ilya Shmulevich (EUSIPCO, 2000)

Perceptual Issues in Music Pattern Recognition: Complexity of Rhythm and Key Finding. - Ilya Shmulevich; Olli Yli-Harja; Edward J. Coyle; Dirk-Jan Povel; Kjell Lemström (Comput. Humanit., 2001)

Breakdown probabilities of recursive stack filters. - Pertti Koivisto; Olli Yli-Harja; Antti Niemistö; Ilya Shmulevich (Signal Process., 2001)

Simplified implementation of the recursive median sieve. - Olli Yli-Harja; Pertti Koivisto; J. Andrew Bangham; Gavin C. Cawley; Richard W. Harvey; Ilya Shmulevich (Signal Process., 2001)

Local entropy estimation in particle velocity images using histogram deconvolution. - Kalle Marjanen; Heimo Ihalainen; Heikki Huttunen; Olli Yli-Harja (Image Processing: Algorithms and Systems, 2002)

Calibration-free methods in segmentation of cDNA microarray images. - Petri Vesanen; Mikko Tiainen; Olli Yli-Harja (Image Processing: Algorithms and Systems, 2002)

On the robustness of the class of stack filters. - Ilya Shmulevich; Olli Yli-Harja; Jaakko Astola; Aleksey D. Korshunov (IEEE Trans. Signal Process., 2002)

Statistical characterization of detail preservation. - Heikki Huttunen; Pertti T. Koivisto; Antti Niemistö; Olli Yli-Harja (Image Processing: Algorithms and Systems, 2003)

Estimation of the distribution type and parameters based on multimodal histograms. - Jari Niemi; Kalle Marjanen; Heimo Ihalainen; Olli Yli-Harja (Image Processing: Algorithms and Systems, 2003)

Estimation of population effects in synchronized budding yeast experiments. - Antti Niemistö; Tommi Aho; Henna Thesleff; Mikko Tiainen; Kalle Marjanen; Marja-Leena Linne; Olli Yli-Harja (Image Processing: Algorithms and Systems, 2003)

Identifying underlying factors in breast cancer using independent component analysis. - John A. Berger; Sampsa Hautaniemi; Henrik Edgren; Outi Monni; Sanjit K. Mitra; Olli Yli-Harja; Jaakko Astola (NNSP, 2003)

Detecting Periodicity in Nonideal Datasets. - Ronald K. Pearson; Harri Lähdesmäki; Heikki Huttunen; Olli Yli-Harja (SDM, 2003)

CGH-Plotter: MATLAB toolbox for CGH-data analysis. - Reija Autio; Sampsa Hautaniemi; Päivikki Kauraniemi; Olli Yli-Harja; Jaakko Astola; Maija Wolf; Anne Kallioniemi (Bioinform., 2003)

A novel strategy for microarray quality control using Bayesian networks. - Sampsa Hautaniemi; Henrik Edgren; Petri Vesanen; Maija Wolf; Anna-Kaarina Järvinen; Olli Yli-Harja; Jaakko Astola; Olli-P. Kallioniemi; Outi Monni (Bioinform., 2003)

Analysis and Visualization of Gene Expression Microarray Data in Human Cancer Using Self-Organizing Maps. - Sampsa Hautaniemi; Olli Yli-Harja; Jaakko Astola; Päivikki Kauraniemi; Anne Kallioniemi; Maija Wolf; Jimmy Ruiz; Spyro Mousses; Olli-P. Kallioniemi (Mach. Learn., 2003)

On Learning Gene Regulatory Networks Under the Boolean Network Model. - Harri Lähdesmäki; Ilya Shmulevich; Olli Yli-Harja (Mach. Learn., 2003)

Estimation and inversion of the effects of cell population asynchrony in gene expression time-series. - Harri Lähdesmäki; Heikki Huttunen; Tommi Aho; Marja-Leena Linne; Jari Niemi; Juha Kesseli; Ronald K. Pearson; Olli Yli-Harja (Signal Process., 2003)

Correction of Misclassifications Using a Proximity-Based Estimation Method. - Antti Niemistö; Ilya Shmulevich; Vladimir Vasilyevich Lukin; Alexander N. Dolia; Olli Yli-Harja (EURASIP J. Adv. Signal Process., 2004)

A strategy for identifying putative causes of gene expression variation in human cancers. - Sampsa Hautaniemi; Markus Ringnér; Päivikki Kauraniemi; Reija Autio; Henrik Edgren; Olli Yli-Harja; Jaakko Astola; Anne Kallioniemi; Olli-Pekka Kallioniemi (J. Frankl. Inst., 2004)

Exploring subjective image quality through isopreference curves. - Antti Lehmussola; Pekka Ruusuvuori; Olli Yli-Harja (ICIP (1), 2005)

Simulation tools for biochemical networks: evaluation of performance and usability. - Antti Pettinen; Tommi Aho; Olli-Pekka Smolander; Tiina Manninen; Antti Saarinen; Kaisa-Leena Taattola; Olli Yli-Harja; Marja-Leena Linne (Bioinform., 2005)

Robust detection of periodic time series measured from biological systems. - Miika Ahdesmäki; Harri Lähdesmäki; Ronald K. Pearson; Heikki Huttunen; Olli Yli-Harja (BMC Bioinform., 2005)

In silico microdissection of microarray data from heterogeneous cell populations. - Harri Lähdesmäki; Ilya Shmulevich; Valerie Dunmire; Olli Yli-Harja; Wei Zhang 011 (BMC Bioinform., 2005)

Robust quantification of in vitro angiogenesis through image analysis. - Antti Niemistö; Valerie Dunmire; Olli Yli-Harja; Wei Zhang 011; Ilya Shmulevich (IEEE Trans. Medical Imaging, 2005)

Extraction of the Number of Peroxisomes in Yeast Cells by Automated Image Analysis. - Antti Niemistö; Jyrki Selinummi; Ramsey Saleem; Ilya Shmulevich; John D. Aitchison; Olli Yli-Harja (EMBC, 2006)

Three-Dimensional Digital Image Analysis of Immunostained Neurons in Thick Tissue Sections. - Jyrki Selinummi; Pekka Ruusuvuori; Antti Lehmussola; Heikki Huttunen; Olli Yli-Harja; Riitta Miettinen (EMBC, 2006)

Learning-based method for spot addressing in microarray images. - Pekka Ruusuvuori; Antti Lehmussola; Olli Yli-Harja (Image Processing: Algorithms and Systems, 2006)

Evaluating the performance of microarray segmentation algorithms. - Antti Lehmussola; Pekka Ruusuvuori; Olli Yli-Harja (Bioinform., 2006)

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

Comparison of automated parameter estimation methods for neuronal signaling networks. - Antti Pettinen; Olli Yli-Harja; Marja-Leena Linne (Neurocomputing, 2006)

Modeling single neuron behavior using stochastic differential equations. - Antti Saarinen; Marja-Leena Linne; Olli Yli-Harja (Neurocomputing, 2006)

Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks. - Harri Lähdesmäki; Sampsa Hautaniemi; Ilya Shmulevich; Olli Yli-Harja (Signal Process., 2006)

Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data. - Miika Ahdesmäki; Harri Lähdesmäki; Andrew Gracey; Ilya Shmulevich; Olli Yli-Harja (BMC Bioinform., 2007)

RMBNToolbox: random models for biochemical networks. - Tommi Aho; Olli-Pekka Smolander; Jari Niemi; Olli Yli-Harja (BMC Syst. Biol., 2007)

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)

Computational Framework for Simulating Fluorescence Microscope Images With Cell Populations. - Antti Lehmussola; Pekka Ruusuvuori; Jyrki Selinummi; Heikki Huttunen; Olli Yli-Harja (IEEE Trans. Medical Imaging, 2007)

sBGMM: A Stratified Beta-Gaussian Mixture Model for Clustering Genes with Multiple Data Sources. - Xiaofeng Dai; Harri Lähdesmäki; Olli Yli-Harja (BIOTECHNO, 2008)

Benchmark set of synthetic images for validating cell image analysis algorithms. - Pekka Ruusuvuori; Antti Lehmussola; Jyrki Selinummi; Tiina Rajala; Heikki Huttunen; Olli Yli-Harja (EUSIPCO, 2008)

Efficient automated method for image-based classification of microbial cells. - Pekka Ruusuvuori; Jenni Seppälä; Timo Erkkilä; Antti Lehmussola; Jaakko A. Puhakka; Olli Yli-Harja (ICPR, 2008)

Synthetic Images of High-Throughput Microscopy for Validation of Image Analysis Methods. - Antti Lehmussola; Pekka Ruusuvuori; Jyrki Selinummi; Tiina Rajala; Olli Yli-Harja (Proc. IEEE, 2008)

Stochastic Differential Equation Model for Cerebellar Granule Cell Excitability. - Antti Saarinen; Marja-Leena Linne; Olli Yli-Harja (PLoS Comput. Biol., 2008)

Towards the experimental evaluation of novel supervised fuzzy adaptive resonance theory for pattern classification. - Alireza Akhbardeh; Nikhil; Perttu E. Koskinen; Olli Yli-Harja (Pattern Recognit. Lett., 2008)

Determining noisy attractors of delayed stochastic gene regulatory networks from multiple data sources. - Xiaofeng Dai; Olli Yli-Harja; Andre S. Ribeiro (Bioinform., 2009)

A joint finite mixture model for clustering genes from independent Gaussian and beta distributed data. - Xiaofeng Dai; Timo Erkkilä; Olli Yli-Harja; Harri Lähdesmäki (BMC Bioinform., 2009)

Delayed Stochastic Model of Transcription at the Single Nucleotide Level. - Andre S. Ribeiro; Olli-Pekka Smolander; Tiina Rajala; Antti Häkkinen; Olli Yli-Harja (J. Comput. Biol., 2009)

Identity verification based on vessel matching from fundus images. - Hannu Oinonen; Heikki Forsvik; Pekka Ruusuvuori; Olli Yli-Harja; Ville Voipio; Heikki Huttunen (ICIP, 2010)

Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images. - Pekka Ruusuvuori; Tarmo Äijö; Sharif Chowdhury; Cecilia Garmendia-Torres; Jyrki Selinummi; Mirko Birbaumer; Aimée M. Dudley; Lucas Pelkmans; Olli Yli-Harja (BMC Bioinform., 2010)

Information propagation within the Genetic Network of Saccharomyces cerevisiae. - Sharif Chowdhury; Jason Lloyd-Price; Olli-Pekka Smolander; Wayne C. V. Baici; Timothy R. Hughes; Olli Yli-Harja; Gordon Chua; Andre S. Ribeiro (BMC Syst. Biol., 2010)

Dynamical effects of transcriptional pause-prone sites. - Andre S. Ribeiro; Antti Häkkinen; Shannon Healy; Olli Yli-Harja (Comput. Biol. Chem., 2010)

Novel Data Fusion Method and Exploration of Multiple Information Sources for Transcription Factor Target Gene Prediction. - Xiaofeng Dai; Olli Yli-Harja; Harri Lähdesmäki (EURASIP J. Adv. Signal Process., 2010)

Effects of Transcriptional Pausing on Gene Expression Dynamics. - Tiina Rajala; Antti Häkkinen; Shannon Healy; Olli Yli-Harja; Andre S. Ribeiro (PLoS Comput. Biol., 2010)

Automatic detection of changes in the dynamics of delayed stochastic gene networks and in vivo production of RNA molecules in Escherichia coli. - Jarno Mäkelä; Heikki Huttunen; Meenakshisundaram Kandhavelu; Olli Yli-Harja; Andre S. Ribeiro (Bioinform., 2011)

Diversity of temporal correlations between genes in models of noisy and noiseless gene networks. - Andre S. Ribeiro; Jason Lloyd-Price; Sharif Chowdhury; Olli Yli-Harja (Biosyst., 2011)

A Beta-Mixture Model for Dimensionality Reduction, Sample Classification and Analysis. - Kirsti Laurila; Bodil Oster; Claus L. Andersen; Philippe Lamy; Torben F. Ørntoft; Olli Yli-Harja; Carsten Wiuf (BMC Bioinform., 2011)

Stochastic sequence-level model of coupled transcription and translation in prokaryotes. - Jarno Mäkelä; Jason Lloyd-Price; Olli Yli-Harja; Andre S. Ribeiro (BMC Bioinform., 2011)

In vivo kinetics of transcription initiation of the lar promoter in Escherichia coli. Evidence for a sequential mechanism with two rate-limiting steps. - Meenakshisundaram Kandhavelu; Henrik Mannerström; Abhishekh Gupta; Antti Häkkinen; Jason Lloyd-Price; Olli Yli-Harja; Andre S. Ribeiro (BMC Syst. Biol., 2011)

Inference of Kinetic Parameters of Delayed Stochastic Models of Gene Expression Using a Markov Chain Approximation. - Henrik Mannerström; Olli Yli-Harja; Andre S. Ribeiro (EURASIP J. Bioinform. Syst. Biol., 2011)

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)

Evolutionary Dynamics of a Population of Cells with a Toxin Suppressor Gene. - Antti Häkkinen; Fred G. Biddle; Olli-Pekka Smolander; Olli Yli-Harja; Andre S. Ribeiro (Trans. Comp. Sys. Biology, 2011)

Sequence Dependent Properties of the Expression Dynamics of Genes and Gene Networks. - Ilya Potapov; Jarno Mäkelä; Olli Yli-Harja; Andre S. Ribeiro (CMSB, 2012)

Effects of Mg2+ on in vivo transcriptional dynamics of the lar promoter. - Meenakshisundaram Kandhavelu; Eero Lihavainen; Anantha Barathi Muthukrishnan; Olli Yli-Harja; Andre Sanches Ribeiro (Biosyst., 2012)

Graph cut and image intensity-based splitting improves nuclei segmentation in high-content screening. - Muhammad Farhan; Pekka Ruusuvuori; Mario Emmenlauer; Pauli Rämö; Olli Yli-Harja; Christoph Dehio (Image Processing: Algorithms and Systems, 2013)

Modeling bioprocess scale-up utilizing regularized linear and logistic regression. - Muhammad Farhan; Antti Larjo; Olli Yli-Harja; Tommi Aho (MLSP, 2013)

ZebIAT, an image analysis tool for registering zebrafish embryos and quantifying cancer metastasis. - Teppo Annila; Eero Lihavainen; Ines J. Marques; Darren R. Williams; Olli Yli-Harja; Andre S. Ribeiro (BMC Bioinform., 2013)

Cell segmentation by multi-resolution analysis and maximum likelihood estimation (MAMLE). - Sharif Chowdhury; Meenakshisundaram Kandhavelu; Olli Yli-Harja; Andre S. Ribeiro (BMC Bioinform., 2013)

Multi-scale Gaussian representation and outline-learning based cell image segmentation. - Muhammad Farhan; Pekka Ruusuvuori; Mario Emmenlauer; Pauli Rämö; Christoph Dehio; Olli Yli-Harja (BMC Bioinform., 2013)

Effects of multimerization on the temporal variability of protein complex abundance. - Antti Häkkinen; Huy Tran; Olli Yli-Harja; Brian P. Ingalls; Andre S. Ribeiro (BMC Syst. Biol., 2013)

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

A novel method for splitting clumps of convex objects incorporating image intensity and using rectangular window-based concavity point-pair search. - Muhammad Farhan; Olli Yli-Harja; Antti Niemistö (Pattern Recognit., 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)

Mathematical Modeling in Systems Biology. - Olli Yli-Harja; Frank Emmert-Streib; Jari Yli-Hietanen (WIVACE, 2016)

Real-time observation of bacterial gene expression noise. - Olga Anufrieva; Adrien Sala; Olli Yli-Harja; Meenakshisundaram Kandhavelu (Nano Commun. Networks, 2016)

A review of connectivity map and computational approaches in pharmacogenomics. - Aliyu Musa; Laleh Soltan Ghoraie; Shu-Dong Zhang; Galina V. Glazko; Olli Yli-Harja; Matthias Dehmer; Benjamin Haibe-Kains; Frank Emmert-Streib (Briefings Bioinform., 2017)

sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters. - Shailesh Tripathi; Jason Lloyd-Price; Andre S. Ribeiro; Olli Yli-Harja; Matthias Dehmer; Frank Emmert-Streib (BMC Bioinform., 2017)

Understanding the World Economy in Terms of Networks: A Survey of Data-Based Network Science Approaches on Economic Networks. - Frank Emmert-Streib; Shailesh Tripathi; Olli Yli-Harja; Matthias Dehmer (Frontiers Appl. Math. Stat., 2018)

Data Analytics Applications for Streaming Data From Social Media: What to Predict? - Frank Emmert-Streib; Olli P. Yli-Harja; Matthias Dehmer (Frontiers Big Data, 2018)

Exploiting Genomic Relations in Big Data Repositories by Graph-Based Search Methods. - Aliyu Musa; Matthias Dehmer; Olli Yli-Harja; Frank Emmert-Streib (Mach. Learn. Knowl. Extr., 2019)

A clarification of misconceptions, myths and desired status of artificial intelligence. - Frank Emmert-Streib; Olli Yli-Harja; Matthias Dehmer (CoRR, 2020)

Artificial Intelligence: A Clarification of Misconceptions, Myths and Desired Status. - Frank Emmert-Streib; Olli Yli-Harja; Matthias Dehmer (Frontiers Artif. Intell., 2020)

Explainable artificial intelligence and machine learning: A reality rooted perspective. - Frank Emmert-Streib; Olli Yli-Harja; Matthias Dehmer (WIREs Data Mining Knowl. Discov., 2020)

Identification of feasible pathway information for c-di-GMP binding proteins in cellulose production. - Syeda Sakira Hassan; Rahul Mangayil; Tommi Aho; Olli Yli-Harja; Matti Karp (CoRR, 2022)

Advanced Scientometric Analysis of Scientific Machine Learning and PINNs: Topic Modeling and Trend Analysis. - Frank Emmert-Streib; Shailesh Tripathi; Amer Farea; Olli Yli-Harja (IEEE Access, 2024)