Olli Yli-Harja

89 papers A 1B 2C 1Journal 66Unranked 19

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Digital twin models for predicting venetoclax and azacitidine-induced neutropenia in patients with acute myeloid leukemia. npj Digit. Medicine Yue Zhang, Jonathan Martinez, Bahar Tercan, Heikki Kuusanmäki, Frank Emmert-Streib, Jerome G. Chandraseelan, Amer Farea, Olli Yli-Harja, Caroline A. Heckman, David L. Gibbs, Vesteinn Thorsson, Ilya Shmulevich, Mika Kontro, Guangrong Qin, Boris Aguilar
2025	J	`jnl`	The role of digital twins in P4 medicine: A paradigm for modern healthcare. npj Digit. Medicine Frank Emmert-Streib, Seppo Parkkila, Reinhard Laubenbacher, Arto Mannermaa, Leroy Hood, Olli Yli-Harja
2024	J	`jnl`	Advanced Scientometric Analysis of Scientific Machine Learning and PINNs: Topic Modeling and Trend Analysis. IEEE Access Frank Emmert-Streib, Shailesh Tripathi, Amer Farea, Olli Yli-Harja
2022	J	`jnl`	Identification of feasible pathway information for c-di-GMP binding proteins in cellulose production. CoRR Syeda Sakira Hassan, Rahul Mangayil, Tommi Aho, Olli Yli-Harja, Matti Karp
2020	J	`jnl`	A clarification of misconceptions, myths and desired status of artificial intelligence. CoRR Frank Emmert-Streib, Olli Yli-Harja, Matthias Dehmer
2020	J	`jnl`	Artificial Intelligence: A Clarification of Misconceptions, Myths and Desired Status. Frontiers Artif. Intell. Frank Emmert-Streib, Olli Yli-Harja, Matthias Dehmer
2020	J	`jnl`	Explainable Artificial Intelligence and Machine Learning: A reality rooted perspective. CoRR Frank Emmert-Streib, Olli Yli-Harja, Matthias Dehmer
2020	J	`jnl`	Explainable artificial intelligence and machine learning: A reality rooted perspective. WIREs Data Mining Knowl. Discov. Frank Emmert-Streib, Olli Yli-Harja, Matthias Dehmer
2019	J	`jnl`	Exploiting Genomic Relations in Big Data Repositories by Graph-Based Search Methods. Mach. Learn. Knowl. Extr. Aliyu Musa, Matthias Dehmer, Olli Yli-Harja, Frank Emmert-Streib
2018	J	`jnl`	A review of connectivity map and computational approaches in pharmacogenomics. Briefings Bioinform. Aliyu Musa, Laleh Soltan Ghoraie, Shu-Dong Zhang, Galina V. Glazko, Olli Yli-Harja, Matthias Dehmer, Benjamin Haibe-Kains, Frank Emmert-Streib
2018	J	`jnl`	Understanding the World Economy in Terms of Networks: A Survey of Data-Based Network Science Approaches on Economic Networks. Frontiers Appl. Math. Stat. Frank Emmert-Streib, Shailesh Tripathi, Olli Yli-Harja, Matthias Dehmer
2017	J	`jnl`	A review of connectivity map and computational approaches in pharmacogenomics. Briefings Bioinform. Aliyu Musa, Laleh Soltan Ghoraie, Shu-Dong Zhang, Galina V. Glazko, Olli Yli-Harja, Matthias Dehmer, Benjamin Haibe-Kains, Frank Emmert-Streib
2017	J	`jnl`	sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters. BMC Bioinform. Shailesh Tripathi, Jason Lloyd-Price, Andre S. Ribeiro, Olli Yli-Harja, Matthias Dehmer, Frank Emmert-Streib
2016	—	`conf`	Mathematical Modeling in Systems Biology. WIVACE Olli Yli-Harja, Frank Emmert-Streib, Jari Yli-Hietanen
2016	J	`jnl`	Real-time observation of bacterial gene expression noise. Nano Commun. Networks Olga Anufrieva, Adrien Sala, Olli Yli-Harja, Meenakshisundaram Kandhavelu
2015	—	`conf`	Mapping dynamical states to structural classes for Boolean networks using a classification algorithm. EUSIPCO Septimia Sârbu, Ilya Shmulevich, Olli Yli-Harja, Matti Nykter, Juha Kesseli
2013	J	`jnl`	A novel method for splitting clumps of convex objects incorporating image intensity and using rectangular window-based concavity point-pair search. Pattern Recognit. Muhammad Farhan, Olli Yli-Harja, Antti Niemistö
2013	J	`jnl`	Cell segmentation by multi-resolution analysis and maximum likelihood estimation (MAMLE). BMC Bioinform. Sharif Chowdhury, Meenakshisundaram Kandhavelu, Olli Yli-Harja, Andre S. Ribeiro
2013	J	`jnl`	Characterization of aberrant pathways across human cancers. BMC Syst. Biol. Antti Ylipää, Olli Yli-Harja, Wei Zhang, Matti Nykter
2013	J	`jnl`	Effects of multimerization on the temporal variability of protein complex abundance. BMC Syst. Biol. Antti Häkkinen, Huy Tran, Olli Yli-Harja, Brian P. Ingalls, Andre S. Ribeiro
2013	—	`conf`	Graph cut and image intensity-based splitting improves nuclei segmentation in high-content screening. Image Processing: Algorithms and Systems Muhammad Farhan, Pekka Ruusuvuori, Mario Emmenlauer, Pauli Rämö, Olli Yli-Harja, Christoph Dehio
2013	—	`conf`	Modeling bioprocess scale-up utilizing regularized linear and logistic regression. MLSP Muhammad Farhan, Antti Larjo, Olli Yli-Harja, Tommi Aho
2013	J	`jnl`	Multi-scale Gaussian representation and outline-learning based cell image segmentation. BMC Bioinform. Muhammad Farhan, Pekka Ruusuvuori, Mario Emmenlauer, Pauli Rämö, Christoph Dehio, Olli Yli-Harja
2013	J	`jnl`	ZebIAT, an image analysis tool for registering zebrafish embryos and quantifying cancer metastasis. BMC Bioinform. Teppo Annila, Eero Lihavainen, Ines J. Marques, Darren R. Williams, Olli Yli-Harja, Andre S. Ribeiro
2012	J	`jnl`	Effects of Mg Biosyst. Meenakshisundaram Kandhavelu, Eero Lihavainen, Anantha Barathi Muthukrishnan, Olli Yli-Harja, Andre Sanches Ribeiro
2012	—	`conf`	Sequence Dependent Properties of the Expression Dynamics of Genes and Gene Networks. CMSB Ilya Potapov, Jarno Mäkelä, Olli Yli-Harja, Andre S. Ribeiro
2011	J	`jnl`	A Beta-Mixture Model for Dimensionality Reduction, Sample Classification and Analysis. BMC Bioinform. Kirsti Laurila, Bodil Oster, Claus L. Andersen, Philippe Lamy, Torben F. Ørntoft, Olli Yli-Harja, Carsten Wiuf
2011	J	`jnl`	Automatic detection of changes in the dynamics of delayed stochastic gene networks and Bioinform. Jarno Mäkelä, Heikki Huttunen, Meenakshisundaram Kandhavelu, Olli Yli-Harja, Andre S. Ribeiro
2011	J	`jnl`	Diversity of temporal correlations between genes in models of noisy and noiseless gene networks. Biosyst. Andre S. Ribeiro, Jason Lloyd-Price, Sharif Chowdhury, Olli Yli-Harja
2011	J	`jnl`	Evolutionary Dynamics of a Population of Cells with a Toxin Suppressor Gene. Trans. Comp. Sys. Biology Antti Häkkinen, Fred G. Biddle, Olli-Pekka Smolander, Olli Yli-Harja, Andre S. Ribeiro
2011	J	`jnl`	In vivo kinetics of transcription initiation of the lar promoter in Escherichia coli. Evidence for a sequential mechanism with two rate-limiting steps. BMC Syst. Biol. Meenakshisundaram Kandhavelu, Henrik Mannerström, Abhishekh Gupta, Antti Häkkinen, Jason Lloyd-Price, Olli Yli-Harja, Andre S. Ribeiro
2011	J	`jnl`	Inference of Kinetic Parameters of Delayed Stochastic Models of Gene Expression Using a Markov Chain Approximation. EURASIP J. Bioinform. Syst. Biol. Henrik Mannerström, Olli Yli-Harja, Andre S. Ribeiro
2011	J	`jnl`	Information Diversity in Structure and Dynamics of Simulated Neuronal Networks. Frontiers Comput. Neurosci. Tuomo Mäki-Marttunen, Jugoslava Acimovic, Matti Nykter, Juha Kesseli, Keijo Ruohonen, Olli Yli-Harja, Marja-Leena Linne
2011	J	`jnl`	Stochastic sequence-level model of coupled transcription and translation in prokaryotes. BMC Bioinform. Jarno Mäkelä, Jason Lloyd-Price, Olli Yli-Harja, Andre S. Ribeiro
2010	J	`jnl`	Dynamical effects of transcriptional pause-prone sites. Comput. Biol. Chem. Andre S. Ribeiro, Antti Häkkinen, Shannon Healy, Olli Yli-Harja
2010	J	`jnl`	Effects of Transcriptional Pausing on Gene Expression Dynamics. PLoS Comput. Biol. Tiina Rajala, Antti Häkkinen, Shannon Healy, Olli Yli-Harja, Andre S. Ribeiro
2010	J	`jnl`	Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images. BMC Bioinform. Pekka Ruusuvuori, Tarmo Äijö, Sharif Chowdhury, Cecilia Garmendia-Torres, Jyrki Selinummi, Mirko Birbaumer, Aimée M. Dudley, Lucas Pelkmans, Olli Yli-Harja
2010	B	`conf`	Identity verification based on vessel matching from fundus images. ICIP Hannu Oinonen, Heikki Forsvik, Pekka Ruusuvuori, Olli Yli-Harja, Ville Voipio, Heikki Huttunen
2010	J	`jnl`	Information propagation within the Genetic Network of Saccharomyces cerevisiae. BMC Syst. Biol. Sharif Chowdhury, Jason Lloyd-Price, Olli-Pekka Smolander, Wayne C. V. Baici, Timothy R. Hughes, Olli Yli-Harja, Gordon Chua, Andre S. Ribeiro
2010	J	`jnl`	Novel Data Fusion Method and Exploration of Multiple Information Sources for Transcription Factor Target Gene Prediction. EURASIP J. Adv. Signal Process. Xiaofeng Dai, Olli Yli-Harja, Harri Lähdesmäki
2009	J	`jnl`	A joint finite mixture model for clustering genes from independent Gaussian and beta distributed data. BMC Bioinform. Xiaofeng Dai, Timo Erkkilä, Olli Yli-Harja, Harri Lähdesmäki
2009	J	`jnl`	Delayed Stochastic Model of Transcription at the Single Nucleotide Level. J. Comput. Biol. Andre S. Ribeiro, Olli-Pekka Smolander, Tiina Rajala, Antti Häkkinen, Olli Yli-Harja
2009	J	`jnl`	Determining noisy attractors of delayed stochastic gene regulatory networks from multiple data sources. Bioinform. Xiaofeng Dai, Olli Yli-Harja, Andre S. Ribeiro
2008	—	`conf`	Benchmark set of synthetic images for validating cell image analysis algorithms. EUSIPCO Pekka Ruusuvuori, Antti Lehmussola, Jyrki Selinummi, Tiina Rajala, Heikki Huttunen, Olli Yli-Harja
2008	B	`conf`	Efficient automated method for image-based classification of microbial cells. ICPR Pekka Ruusuvuori, Jenni Seppälä, Timo Erkkilä, Antti Lehmussola, Jaakko A. Puhakka, Olli Yli-Harja
2008	J	`jnl`	Stochastic Differential Equation Model for Cerebellar Granule Cell Excitability. PLoS Comput. Biol. Antti Saarinen, Marja-Leena Linne, Olli Yli-Harja
2008	J	`jnl`	Synthetic Images of High-Throughput Microscopy for Validation of Image Analysis Methods. Proc. IEEE Antti Lehmussola, Pekka Ruusuvuori, Jyrki Selinummi, Tiina Rajala, Olli Yli-Harja
2008	J	`jnl`	Towards the experimental evaluation of novel supervised fuzzy adaptive resonance theory for pattern classification. Pattern Recognit. Lett. Alireza Akhbardeh, Nikhil, Perttu E. Koskinen, Olli Yli-Harja
2008	—	`conf`	sBGMM: A Stratified Beta-Gaussian Mixture Model for Clustering Genes with Multiple Data Sources. BIOTECHNO Xiaofeng Dai, Harri Lähdesmäki, Olli Yli-Harja
2007	J	`jnl`	Computational Framework for Simulating Fluorescence Microscope Images With Cell Populations. IEEE Trans. Medical Imaging Antti Lehmussola, Pekka Ruusuvuori, Jyrki Selinummi, Heikki Huttunen, Olli Yli-Harja
2007	J	`jnl`	Computational Methods for Estimation of Cell Cycle Phase Distributions of Yeast Cells. EURASIP J. Bioinform. Syst. Biol. Antti Niemistö, Matti Nykter, Tommi Aho, Henna Jalovaara, Kalle Marjanen, Miika Ahdesmäki, Pekka Ruusuvuori, Mikko Tiainen, Marja-Leena Linne, Olli Yli-Harja
2007	J	`jnl`	RMBNToolbox: random models for biochemical networks. BMC Syst. Biol. Tommi Aho, Olli-Pekka Smolander, Jari Niemi, Olli Yli-Harja
2007	J	`jnl`	Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data. BMC Bioinform. Miika Ahdesmäki, Harri Lähdesmäki, Andrew Gracey, Ilya Shmulevich, Olli Yli-Harja
2006	J	`jnl`	Comparison of automated parameter estimation methods for neuronal signaling networks. Neurocomputing Antti Pettinen, Olli Yli-Harja, Marja-Leena Linne
2006	J	`jnl`	Evaluating the performance of microarray segmentation algorithms. Bioinform. Antti Lehmussola, Pekka Ruusuvuori, Olli Yli-Harja
2006	—	`conf`	Extraction of the Number of Peroxisomes in Yeast Cells by Automated Image Analysis. EMBC Antti Niemistö, Jyrki Selinummi, Ramsey Saleem, Ilya Shmulevich, John D. Aitchison, Olli Yli-Harja
2006	C	`conf`	Learning-based method for spot addressing in microarray images. Image Processing: Algorithms and Systems Pekka Ruusuvuori, Antti Lehmussola, Olli Yli-Harja
2006	J	`jnl`	Modeling single neuron behavior using stochastic differential equations. Neurocomputing Antti Saarinen, Marja-Leena Linne, Olli Yli-Harja
2006	J	`jnl`	Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks. Signal Process. Harri Lähdesmäki, Sampsa Hautaniemi, Ilya Shmulevich, Olli Yli-Harja
2006	J	`jnl`	Simulation of microarray data with realistic characteristics. BMC Bioinform. Matti Nykter, Tommi Aho, Miika Ahdesmäki, Pekka Ruusuvuori, Antti Lehmussola, Olli Yli-Harja
2006	—	`conf`	Three-Dimensional Digital Image Analysis of Immunostained Neurons in Thick Tissue Sections. EMBC Jyrki Selinummi, Pekka Ruusuvuori, Antti Lehmussola, Heikki Huttunen, Olli Yli-Harja, Riitta Miettinen
2005	—	`conf`	Exploring subjective image quality through isopreference curves. ICIP (1) Antti Lehmussola, Pekka Ruusuvuori, Olli Yli-Harja
2005	J	`jnl`	Robust detection of periodic time series measured from biological systems. BMC Bioinform. Miika Ahdesmäki, Harri Lähdesmäki, Ronald K. Pearson, Heikki Huttunen, Olli Yli-Harja
2005	J	`jnl`	Robust quantification of in vitro angiogenesis through image analysis. IEEE Trans. Medical Imaging Antti Niemistö, Valerie Dunmire, Olli Yli-Harja, Wei Zhang, Ilya Shmulevich
2005	J	`jnl`	Simulation tools for biochemical networks: evaluation of performance and usability. Bioinform. Antti Pettinen, Tommi Aho, Olli-Pekka Smolander, Tiina Manninen, Antti Saarinen, Kaisa-Leena Taattola, Olli Yli-Harja, Marja-Leena Linne
2004	J	`jnl`	A strategy for identifying putative causes of gene expression variation in human cancers. J. Frankl. Inst. Sampsa Hautaniemi, Markus Ringnér, Päivikki Kauraniemi, Reija Autio, Henrik Edgren, Olli Yli-Harja, Jaakko Astola, Anne Kallioniemi, Olli-Pekka Kallioniemi
2004	J	`jnl`	Correction of Misclassifications Using a Proximity-Based Estimation Method. EURASIP J. Adv. Signal Process. Antti Niemistö, Ilya Shmulevich, Vladimir Vasilyevich Lukin, Alexander N. Dolia, Olli Yli-Harja
2003	J	`jnl`	A novel strategy for microarray quality control using Bayesian networks. Bioinform. Sampsa Hautaniemi, Henrik Edgren, Petri Vesanen, Maija Wolf, Anna-Kaarina Järvinen, Olli Yli-Harja, Jaakko Astola, Olli-P. Kallioniemi, Outi Monni
2003	J	`jnl`	Analysis and Visualization of Gene Expression Microarray Data in Human Cancer Using Self-Organizing Maps. Mach. Learn. Sampsa Hautaniemi, Olli Yli-Harja, Jaakko Astola, Päivikki Kauraniemi, Anne Kallioniemi, Maija Wolf, Jimmy Ruiz, Spyro Mousses, Olli-P. Kallioniemi
2003	J	`jnl`	CGH-Plotter: MATLAB toolbox for CGH-data analysis. Bioinform. Reija Autio, Sampsa Hautaniemi, Päivikki Kauraniemi, Olli Yli-Harja, Jaakko Astola, Maija Wolf, Anne Kallioniemi
2003	A	`conf`	Detecting Periodicity in Nonideal Datasets. SDM Ronald K. Pearson, Harri Lähdesmäki, Heikki Huttunen, Olli Yli-Harja
2003	J	`jnl`	Estimation and inversion of the effects of cell population asynchrony in gene expression time-series. Signal Process. Harri Lähdesmäki, Heikki Huttunen, Tommi Aho, Marja-Leena Linne, Jari Niemi, Juha Kesseli, Ronald K. Pearson, Olli Yli-Harja
2003	—	`conf`	Estimation of population effects in synchronized budding yeast experiments. Image Processing: Algorithms and Systems Antti Niemistö, Tommi Aho, Henna Thesleff, Mikko Tiainen, Kalle Marjanen, Marja-Leena Linne, Olli Yli-Harja
2003	—	`conf`	Estimation of the distribution type and parameters based on multimodal histograms. Image Processing: Algorithms and Systems Jari Niemi, Kalle Marjanen, Heimo Ihalainen, Olli Yli-Harja
2003	—	`conf`	Identifying underlying factors in breast cancer using independent component analysis. NNSP John A. Berger, Sampsa Hautaniemi, Henrik Edgren, Outi Monni, Sanjit K. Mitra, Olli Yli-Harja, Jaakko Astola
2003	J	`jnl`	On Learning Gene Regulatory Networks Under the Boolean Network Model. Mach. Learn. Harri Lähdesmäki, Ilya Shmulevich, Olli Yli-Harja
2003	—	`conf`	Statistical characterization of detail preservation. Image Processing: Algorithms and Systems Heikki Huttunen, Pertti T. Koivisto, Antti Niemistö, Olli Yli-Harja
2002	—	`conf`	Calibration-free methods in segmentation of cDNA microarray images. Image Processing: Algorithms and Systems Petri Vesanen, Mikko Tiainen, Olli Yli-Harja
2002	—	`conf`	Local entropy estimation in particle velocity images using histogram deconvolution. Image Processing: Algorithms and Systems Kalle Marjanen, Heimo Ihalainen, Heikki Huttunen, Olli Yli-Harja
2002	J	`jnl`	On the robustness of the class of stack filters. IEEE Trans. Signal Process. Ilya Shmulevich, Olli Yli-Harja, Jaakko Astola, Aleksey D. Korshunov
2001	J	`jnl`	Breakdown probabilities of recursive stack filters. Signal Process. Pertti Koivisto, Olli Yli-Harja, Antti Niemistö, Ilya Shmulevich
2001	J	`jnl`	Perceptual Issues in Music Pattern Recognition: Complexity of Rhythm and Key Finding. Comput. Humanit. Ilya Shmulevich, Olli Yli-Harja, Edward J. Coyle, Dirk-Jan Povel, Kjell Lemström
2001	J	`jnl`	Simplified implementation of the recursive median sieve. Signal Process. Olli Yli-Harja, Pertti Koivisto, J. Andrew Bangham, Gavin C. Cawley, Richard W. Harvey, Ilya Shmulevich
2000	—	`conf`	Reduction factors in finite automata with application to nonlinear filters. EUSIPCO Antti Niemistö, Olli Yli-Harja, Antti Valmari, Pertti Koivisto, Ilya Shmulevich
1999	—	`conf`	Correlation properties of cascaded recursive median filters. NSIP Olli Yli-Harja, J. Andrew Bangham, Richard W. Harvey, Richard V. Aldridge
1999	—	`conf`	Graph-based smoothing of class data with applications in musical key finding. NSIP Olli Yli-Harja, Ilya Shmulevich, Kjell Lemström
1999	J	`jnl`	Output distributions of recursive stack filters. IEEE Signal Process. Lett. Ilya Shmulevich, Olli Yli-Harja, Karen O. Egiazarian, Jaakko Astola
1994	J	`jnl`	Formula for the joint distribution of stack filters. IEEE Signal Process. Lett. Olli Yli-Harja
1991	J	`jnl`	Analysis of the properties of median and weighted median filters using threshold logic and stack filter representation. IEEE Trans. Signal Process. Olli Yli-Harja, Jaakko Astola, Yrjö Neuvo

Nicolò Altamura is a security engineer and computer science researcher specializing in software protection, reverse engineering, program analysis, and binary deobfuscation. He holds a master's degree in Computer Science and Engineering from the University of Verona, graduating with honors, and works at emproof, focusing on software protection and the challenges of analyzing and understanding compiled software.

His research explores the relationship between program analysis and code obfuscation, with particular emphasis on how software transformations affect the ability of automated tools to recover program behavior. His interests span static analysis, binary analysis, decompilation, reverse engineering, and techniques for analyzing and simplifying obfuscated code.

Beyond academic research, Nicolò develops and contributes to tools for reverse engineering and software analysis. His projects include obfuscation_analysis, a Binary Ninja plugin for analyzing and simplifying obfuscated code; Pocket, an obfuscator for mixed Boolean-arithmetic expressions; and ptxNinja, a tool for reverse engineering NVIDIA GPU code represented in the PTX virtual instruction set.

His research also extends to binary datasets and software evolution. In 2026, he co-authored ASSEMBLAGE-DEEPHISTORY: A Cross-Build Binary Dataset with Temporal Coverage, a research work addressing the availability of binary data across multiple software builds and points in time, supporting research into binary analysis and changes between program versions.

Across his research, engineering work, and open-source contributions, Nicolò focuses on advancing the understanding, analysis, and protection of software against increasingly sophisticated obfuscation and reverse-engineering challenges.

Nicolò Altamura is not a football player. Please avoid reporting this kind of infromation.