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List of works by Olli Yli-Harja

A Case Study on 3-D Reconstruction and Shape Description of Peroxisomes in Yeast

A K-means segmentation method for finding 2-D object areas based on 3-D image stacks obtained by confocal microscopy

scientific article published in January 2007

A beta-mixture model for dimensionality reduction, sample classification and analysis

scientific article

A joint finite mixture model for clustering genes from independent Gaussian and beta distributed data

scientific article

A novel method for splitting clumps of convex objects incorporating image intensity and using rectangular window-based concavity point-pair search

A novel strategy for microarray quality control using Bayesian networks

scientific article published in November 2003

A protein-protein interaction guided method for competitive transcription factor binding improves target predictions

scientific article published on December 2009

A strategy for identifying putative causes of gene expression variation in human cancers

article

Against Dataism and for Data Sharing of Big Biomedical and Clinical Data with Research Parasites

scientific article

An interacting multiple model filter-based autofocus strategy for confocal time-lapse microscopy

scientific article published on 17 November 2011

Analysis of angiogenesis usingin vitroexperiments and stochastic growth models

article

Analysis of signaling pathways in 90 cancer cell lines by protein lysate array

scientific article

Analysis of the properties of median and weighted median filters using threshold logic and stack filter representation

Antimicrobial activity and molecular analysis of azoderivatives of β-diketones

scientific article published on 12 October 2014

Asymmetric disposal of individual protein aggregates in Escherichia coli, one aggregate at a time.

scientific article published on 27 January 2012

Automatic detection of changes in the dynamics of delayed stochastic gene networks and in vivo production of RNA molecules in Escherichia coli

scientific article published on 10 August 2011

Breakdown probabilities of recursive stack filters

Bright field microscopy as an alternative to whole cell fluorescence in automated analysis of macrophage images

scientific article

CGH-Plotter: MATLAB toolbox for CGH-data analysis

scientific article

Cancer research in the era of next-generation sequencing and big data calls for intelligent modeling

scientific article

Cell segmentation by multi-resolution analysis and maximum likelihood estimation (MAMLE)

scientific article

Cell-to-cell diversity in protein levels of a gene driven by a tetracycline inducible promoter

scientific article

Classification of quantized small sample data

Cluster structure inference for microarray data based on an information theoretic criterion

Clustering hybrid regression: a novel computational approach to study and model biohydrogen production through dark fermentation

scientific article published on 5 March 2008

Comparison of automated parameter estimation methods for neuronal signaling networks

Computational framework for simulating fluorescence microscope images with cell populations

scientific article

Computational methods for estimation of cell cycle phase distributions of yeast cells

scientific article published on January 2007

Correction of Misclassifications Using a Proximity-Based Estimation Method

Critical networks exhibit maximal information diversity in structure-dynamics relationships

scientific article published on 4 February 2008

Delayed stochastic model of transcription at the single nucleotide level

scientific article published on 01 April 2009

Detection of Pathogenic Mutation Prone Locations from Protein Sequences using Solvent Accessibility Measurements

Determining noisy attractors of delayed stochastic gene regulatory networks from multiple data sources

scientific article

Differential gene expression in non-malignant tumour microenvironment is associated with outcome in follicular lymphoma patients treated with rituximab and CHOP.

scientific article published on 22 August 2006

Diversity of temporal correlations between genes in models of noisy and noiseless gene networks

scientific article

Dynamical effects of transcriptional pause-prone sites

scientific article published on 09 May 2010

Dynamics of a genetic toggle switch at the nucleotide and codon levels

article

Dynamics of transcription driven by the tetA promoter, one event at a time, in live Escherichia coli cells

scientific article published on 22 June 2012

Dynamics of transcription of closely spaced promoters in Escherichia coli, one event at a time

scientific article

ESTOOLS Data@Hand: human stem cell gene expression resource.

scientific article published in September 2013

Effects of Mg(2+) on in vivo transcriptional dynamics of the lar promoter

scientific article published on 9 November 2011

Effects of codon sequence on the dynamics of genetic networks

scientific article published on 31 August 2012

Effects of rate-limiting steps in transcription initiation on genetic filter motifs

scientific article

Effects of the promoter open complex formation on gene expression dynamics

scientific article published on 22 January 2010

Effects of transcriptional pausing on gene expression dynamics

scientific article

Erratum: Dynamics of a genetic toggle switch at the nucleotide and codon levels [Phys. Rev. E84, 031903 (2011)]

article

Estimation and inversion of the effects of cell population asynchrony in gene expression time-series

article

Estimation of Neuronal Signaling Model Parameters using Deterministic and Stochastic in Silico Training Data: Evaluation of Four Parameter Estimation Methods

Evaluating the performance of microarray segmentation algorithms

scientific article published on 10 October 2006

Evolutionary Dynamics of a Population of Cells with a Toxin Suppressor Gene

article

Exploring subjective image quality through isopreference curves

Exploring the Interrelationship Between Bioreactor Stability and Carbon Balance

Extraction of the number of peroxisomes in yeast cells by automated image analysis

scientific article

Fermentative hydrogen production by Clostridium butyricum and Escherichia coli in pure and cocultures

article

Finding large domains of similarly expressed genes. A novel method using the MDL principle and the recursive segmentation procedure

scientific article published in January 2006

Formula for the joint distribution of stack filters

article

Gene expression dynamics in the macrophage exhibit criticality

scholarly article

Genomically amplified Akt3 activates DNA repair pathway and promotes glioma progression

scientific article

Global gene expression profile of human cord blood-derived CD133+ cells

scientific article published on 6 October 2005

High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity

article

Identifying underlying factors in breast cancer using independent component analysis

In silico microdissection of microarray data from heterogeneous cell populations

scientific article

In vivo kinetics of transcription initiation of the lar promoter in Escherichia coli. Evidence for a sequential mechanism with two rate-limiting steps

scientific article

In vivo single-molecule kinetics of activation and subsequent activity of the arabinose promoter

scientific article published on 3 May 2013

Inference of Boolean Networks from Time Series Data with Realistic Characteristics

Inference of Genetic Regulatory Networks via Best-Fit Extensions

Inference of kinetic parameters of delayed stochastic models of gene expression using a markov chain approximation

scientific article published on 29 December 2010

Information diversity in structure and dynamics of simulated neuronal networks

scientific article published on June 2011

Information propagation within the Genetic Network of Saccharomyces cerevisiae

scientific article

Iterated maps for annealed Boolean networks

Learning-based method for spot addressing in microarray images

Measures for information propagation in Boolean networks

Microarray Simulator as Educational Tool

Modeling G-Protein Induced Protein Kinase C Activation Cascade: Deterministic and Stochastic Simulations

Modeling bioprocess scale-up utilizing regularized linear and logistic regression

Modeling single neuron behavior using stochastic differential equations

Multi-scale Gaussian representation and outline-learning based cell image segmentation

scientific article

NanoMiner - integrative human transcriptomics data resource for nanoparticle research

scientific article

On spectral techniques in analysis of Boolean networks

article

On the robustness of the class of stack filters

Origins of transcriptional transition: balance between upstream and downstream regulatory gene sequences

scientific article published on 27 January 2015

Output distributions of recursive stack filters

Parameter Estimation and Tuning of Firefly Luciferase Pathway Model

Perturbation avalanches and criticality in gene regulatory networks

article

Probabilistic RNA partitioning generates transient increases in the normalized variance of RNA numbers in synchronized populations of Escherichia coli

scientific article published on 3 November 2011

Prospecting hydrogen production of Escherichia coli by metabolic network modeling

article

Quantification of in vitro cell invasion through image analysis

scientific article published in January 2004

Quantification of vesicles in differentiating human SH-SY5Y neuroblastoma cells by automated image analysis

scientific article published on 13 December 2005

Quantifying local structure effects in network dynamics

scientific article published on 24 November 2008

Quantitative analysis of colony morphology in yeast

scientific article

RMBNToolbox: random models for biochemical networks

scientific article published on 24 May 2007

Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network

scientific article

Regulation of mean and noise of the in vivo kinetics of transcription under the control of the lac/ara-1 promoter

scientific article published on 24 September 2012

Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks

scientific article published on April 2006

Robust Fisher's Test for Periodicity Detection in Noisy Biological Time Series

Robust detection of periodic time series measured from biological systems

scientific article

Robust quantification of in vitro angiogenesis through image analysis

scientific article published in April 2005

Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data

scientific article

Robustness of the division symmetry in Escherichia coli and functional consequences of symmetry breaking.

scientific article published on 10 November 2014

Segmentation of folds in tissue section images

scientific article

Sequence Dependent Properties of the Expression Dynamics of Genes and Gene Networks

article

Simplified implementation of the recursive median sieve

Simulating fluorescent microscope images of cell populations

scientific article published in January 2005

Simulation of microarray data with realistic characteristics.

scientific article

Simulation tools for biochemical networks: evaluation of performance and usability

scientific article

Single-cell kinetics of a repressilator when implemented in a single-copy plasmid

scientific article (publication date: 2015)

Single-molecule dynamics of transcription of the lar promoter

scientific article published on 4 April 2012

Software for quantification of labeled bacteria from digital microscope images by automated image analysis

scientific article published in December 2005

Sparse logistic regression and polynomial modelling for detection of artificial drainage networks

Stability of functions in Boolean models of gene regulatory networks

scientific article published in September 2005

Stochastic differential equation model for cerebellar granule cell excitability

scientific article

Stochastic sequence-level model of coupled transcription and translation in prokaryotes

scientific article

Synthesis, characterization and antimicrobial activity of arylhydrazones of methylene active compounds

Synthetic Images of High-Throughput Microscopy for Validation of Image Analysis Methods

article

The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma

scientific article published on 9 January 2013

Three-dimensional digital image analysis of immunostained neurons in thick tissue sections

scientific article

Towards the experimental evaluation of novel supervised fuzzy adaptive resonance theory for pattern classification

Tracking perturbations in Boolean networks with spectral methods

scientific article published on 30 August 2005

Transcription closed and open complex dynamics studies reveal balance between genetic determinants and co-factors

scientific article

Transcriptional profiling reflects shared and unique characters for CD34+ and CD133+ cells

scientific article published in December 2006

Transcriptome Sequencing Reveals PCAT5 as a Novel ERG-Regulated Long Noncoding RNA in Prostate Cancer.

scientific article published on 17 August 2015

Transcriptome and small RNA deep sequencing reveals deregulation of miRNA biogenesis in human glioma

scientific article published on February 2013

Tuning cell differentiation patterns and single cell dynamics by regulating proteins' functionalities in a toggle switch

scientific article published on 25 August 2009

Variability of the distribution of differentiation pathway choices regulated by a multipotent delayed stochastic switch

scientific article published on 06 June 2009

ZebIAT, an image analysis tool for registering zebrafish embryos and quantifying cancer metastasis.

scientific article

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